X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 292.0
Details 0.1 M sodium citrate pH 5.5, 16% PEG 4000, 15% 2-propanol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.6 α = 90
b = 71.6 β = 90
c = 197.79 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2012-09-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-3 0.979 MAX II I911-3

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.6 30 99.8 0.06 -- -- 5.9 34882 34817 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.6 2.65 99.8 0.75 -- 2.1 5.9 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 2.65 29.584 -- 1.39 -- 32875 3316 99.87 -- 0.1986 0.1941 0.2383 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.6501 2.688 -- 136 1252 0.305 0.3269 -- 100.0
X Ray Diffraction 2.688 2.7281 -- 126 1191 -- -- -- 100.0
X Ray Diffraction 2.7281 2.7707 -- 146 1230 0.2634 0.3351 -- 100.0
X Ray Diffraction 2.7707 2.816 -- 140 1252 0.2592 0.3443 -- 100.0
X Ray Diffraction 2.816 2.8646 -- 140 1289 0.2727 0.3563 -- 100.0
X Ray Diffraction 2.8646 2.9166 -- 122 1185 0.2792 0.3305 -- 100.0
X Ray Diffraction 2.9166 2.9727 -- 148 1234 0.2543 0.3782 -- 100.0
X Ray Diffraction 2.9727 3.0333 -- 144 1209 0.2476 0.2954 -- 100.0
X Ray Diffraction 3.0333 3.0992 -- 133 1271 0.2482 0.3149 -- 100.0
X Ray Diffraction 3.0992 3.1712 -- 140 1196 0.2338 0.3557 -- 100.0
X Ray Diffraction 3.1712 3.2504 -- 144 1281 0.2303 0.299 -- 100.0
X Ray Diffraction 3.2504 3.3382 -- 128 1185 0.236 0.2942 -- 100.0
X Ray Diffraction 3.3382 3.4362 -- 142 1254 0.2081 0.2511 -- 100.0
X Ray Diffraction 3.4362 3.547 -- 134 1221 0.2195 0.3039 -- 100.0
X Ray Diffraction 3.547 3.6735 -- 138 1197 0.1996 0.2714 -- 100.0
X Ray Diffraction 3.6735 3.8203 -- 152 1274 0.198 0.2672 -- 100.0
X Ray Diffraction 3.8203 3.9938 -- 140 1230 0.1883 0.2115 -- 100.0
X Ray Diffraction 3.9938 4.2038 -- 136 1248 0.1716 0.2394 -- 100.0
X Ray Diffraction 4.2038 4.4663 -- 140 1225 0.1649 0.1849 -- 100.0
X Ray Diffraction 4.4663 4.8098 -- 138 1229 0.1392 0.1691 -- 100.0
X Ray Diffraction 4.8098 5.2914 -- 141 1217 0.1451 0.1897 -- 100.0
X Ray Diffraction 5.2914 6.0514 -- 128 1234 0.1828 0.1834 -- 100.0
X Ray Diffraction 6.0514 7.6026 -- 132 1247 0.1824 0.223 -- 100.0
X Ray Diffraction 7.6026 29.5858 -- 148 1208 0.1747 0.1932 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.63
f_bond_d 0.003
f_angle_d 0.706
f_plane_restr 0.004
f_chiral_restr 0.044
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3056
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 16

Software

Software
Software Name Purpose
PHENIX refinement version: (phenix.refine: 1.8_1069)
XDS data reduction
XSCALE data scaling
PHENIX phasing