The "horiz" direction is along the spindle axis, "thick" is the direction along the beam path, and "vert" is generally the direction of gravity at a synchrotron.
The "rotisserie factor" is an estimate of the total exposed
volume of the crystal over the whole data set relative to the volume that
would be exposed if the crystal was
perfectly still during the data collection.
Specifically, If the crystal is bigger in the beam in the "vert" or "thick" directions, then this will tend to spread out the dose as the crystal rotates. 180 degrees of total rotation is assumed here. If your beam is too hot to get 180 shots, you will get a dialog box reminding you that the attenuation has been automatically adjusted. Shorter wedges will have more apparent damage due to the perfectly good crystal that never passes into the x-ray beam.
Also, if the crystal has non-zero "translation during dataset" along the "horiz" axis, this will also tend to spread out the damage.
The net effect of moving diffractive crystal volume in and out of the beam during data collection and then merging all data in the end is to increase the effective size of the x-ray beam, albeit without the even dose distribution one would obtain with a crystal-matching beam. Dose contrast effects that result from damage in in one part of the crystal propagating into other parts is not implemented here.
The kdose value is computed from the wavelength using the formula given in Holton (2009). It assumes negligible heavy metal content in the crystal. For more accurate values, use raddose.
Note that flux and beam size values are taken from BioSync and these entries do not always mention the wavelength. In such cases 1 A radiation is assumed. Beamline flux also tends to change significantly with wavelength, so for the most accurate values, ask your local beamline scientist!
10 MGy/A resolution:
Howells MR, Beetz T, Chapman HN, Cui C, Holton JM, Jacobsen CJ, Kirz J, Lima E, Marchesini S, Miao H, Sayre D, Shapiro DA, Spence JHC & Starodub D (2009)."An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy", J. Electron Spectrosc. Relat. Phenom. 170, 4-12.
1% non-isomorphism per MGy:
Banumathi S, Zwart PH, Ramagopal UA, Dauter M & Dauter Z (2004)."Structural effects of radiation damage and its potential for phasing", Acta Cryst. D 60, 1085-1093.
200 kGy for Room Temperature:
Warkentin M, Badeau R, Hopkins JB, Mulichak AM, Keefe LJ & Thorne RE (2012)."Global radiation damage at 300 and 260 K with dose rates approaching 1 MGy s-1", Acta Cryst. D 68, 124-133.
Barker AI, Southworth-Davies RJ, Paithankar KS, Carmichael I & Garman EF (2009)."Room-temperature scavengers for macromolecular crystallography: increased lifetimes and modified dose dependence of the intensity decay", J. Sync. Rad. 16, 205-216.
Blake CCF & Phillips DC (1962). Biological Effects of Ionizing radiation at the Molecular Level, pp. 183-191. Vienna: IAEA.
5 MGy for Se-Met:
Holton JM (2007)."XANES measurements of the rate of radiation damage to selenomethionine side chains", J. Synch. Rad. 14, 51-72.
4 MGy for Hg-Cys:
Ramagopal UA, Dauter Z, Thirumuruhan R, Fedorov E & Almo SC (2005)."Radiation-induced site-specific damage of mercury derivatives: phasing and implications", Acta Cryst. D 61, 1289-1298.
2 MGy for Cys-Cys:
Murray JW & Garman EF (2002)."Investigation of possible free-radical scavengers and metrics for radiation damage in protein cryocrystallography", J. Sync. Rad. 9, 347-354.
500 kGy for Br-RNA:
Olieric V, Ennifar E, Meents A, Fleurant M, Besnard C, Pattison P, Schiltz M, Schulze-Briese C & Dumas P (2007)."Using X-ray absorption spectra to monitor specific radiation damage to anomalously scattering atoms in macromolecular crystallography", Acta Cryst. D 63, 759-768.
500 kGy for Photosystem II:
Yano J, Kern J, Irrgang K-D, Latimer MJ, Bergmann U, Glatzel P, Pushkar Y, Biesiadka J, Loll B, Sauer K, Messinger J, Zouni A & Yachandra VK (2005)."X-ray damage to the Mn4Ca complex in single crystals of photosystem II: A case study for metalloprotein crystallography", PNAS USA 102, 12047-12052.
60 kGy for putidaredoxin:
Corbett MC, Latimer MJ, Poulos TL, Sevrioukova IF, Hodgson KO & Hedman B (2007)."Photoreduction of the active site of the metalloprotein putidaredoxin by synchrotron radiation", Acta Cryst. D 63, 951-960.
60 kGy for bacteriorhodopsin:
Borshchevskiy V, Round E, Erofeev I, Weik M, Ishchenko A, Gushchin I, Mishin A, Willbold D, Buldt G & Gordeliy V (2014)."Low-dose X-ray radiation induces structural alterations in proteins", Acta Cryst. D 70, 2675-2685.
20 kGy for Fe reduction in myoglobin:
Denisov IG, Victoria DC & Sligar SG (2007)."Cryoradiolytic reduction of heme proteins: Maximizing dose dependent yield", Radiat Phys Chem Oxf Engl 1993 76, 714-721.
rough rotisserie factor:
Holton JM (2009)."A beginner's guide to radiation damage", J. Synch. Rad. 16, 133-142.
more accurate rotisserie factor calculations:
Zeldin OB, Brockhauser S, Bremridge J, Holton JM & Garman EF (2013)."Predicting the X-ray lifetime of protein crystals", PNAS USA 110, 20551-20556.