X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.8
Temperature 293.0
Details 20% (w/v) PEG 3350, 50 mM Ches, 200 mM magnesium formate dihydrate, pH 8.8, vapor diffusion, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 139.37 α = 90
b = 69.56 β = 100.12
c = 232.32 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
pixel DECTRIS PILATUS 6M -- 2011-10-16
Diffraction Radiation
Monochromator Protocol
-- Single Wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID

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
2.2 228.7 98.2 0.087 -- -- 3.5 109337 109337 0.0 -3.0 --
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)
2.2 2.24 97.7 0.668 -- 2.0 3.6 5397

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
MOLECULAR REPLACEMENT 2.2 38.624 -- 1.84 -- 109316 5497 97.94 -- 0.1686 0.1658 0.2231 RANDOM
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 2.2 2.225 -- 190 3471 0.2385 0.2988 -- 98.0
X Ray Diffraction 2.225 2.2512 -- 206 3364 0.2266 0.3027 -- 97.0
X Ray Diffraction 2.2512 2.2786 -- 172 3430 0.2304 0.2977 -- 98.0
X Ray Diffraction 2.2786 2.3075 -- 170 3421 0.2263 0.2864 -- 97.0
X Ray Diffraction 2.3075 2.3378 -- 190 3386 0.2203 0.2949 -- 98.0
X Ray Diffraction 2.3378 2.3699 -- 197 3440 0.2036 0.2493 -- 98.0
X Ray Diffraction 2.3699 2.4037 -- 189 3423 0.2024 0.2724 -- 98.0
X Ray Diffraction 2.4037 2.4396 -- 180 3439 0.2011 0.3277 -- 98.0
X Ray Diffraction 2.4396 2.4777 -- 194 3380 0.2098 0.2699 -- 98.0
X Ray Diffraction 2.4777 2.5183 -- 177 3492 0.2021 0.2889 -- 98.0
X Ray Diffraction 2.5183 2.5617 -- 196 3414 0.1969 0.2763 -- 98.0
X Ray Diffraction 2.5617 2.6083 -- 172 3436 0.1909 0.242 -- 98.0
X Ray Diffraction 2.6083 2.6585 -- 170 3438 0.1855 0.262 -- 98.0
X Ray Diffraction 2.6585 2.7127 -- 166 3459 0.1861 0.2714 -- 98.0
X Ray Diffraction 2.7127 2.7717 -- 200 3480 0.1917 0.2779 -- 98.0
X Ray Diffraction 2.7717 2.8361 -- 171 3407 0.1933 0.2928 -- 98.0
X Ray Diffraction 2.8361 2.907 -- 201 3506 0.1863 0.2539 -- 98.0
X Ray Diffraction 2.907 2.9856 -- 179 3474 0.1766 0.2256 -- 98.0
X Ray Diffraction 2.9856 3.0734 -- 188 3413 0.1761 0.2522 -- 98.0
X Ray Diffraction 3.0734 3.1726 -- 189 3483 0.1684 0.215 -- 98.0
X Ray Diffraction 3.1726 3.2859 -- 192 3467 0.1696 0.2178 -- 98.0
X Ray Diffraction 3.2859 3.4174 -- 189 3447 0.1681 0.2386 -- 98.0
X Ray Diffraction 3.4174 3.5728 -- 173 3497 0.1564 0.2138 -- 98.0
X Ray Diffraction 3.5728 3.761 -- 171 3473 0.1466 0.211 -- 99.0
X Ray Diffraction 3.761 3.9965 -- 182 3489 0.143 0.1813 -- 98.0
X Ray Diffraction 3.9965 4.3047 -- 180 3525 0.1399 0.1798 -- 98.0
X Ray Diffraction 4.3047 4.7372 -- 162 3493 0.1214 0.1517 -- 98.0
X Ray Diffraction 4.7372 5.421 -- 175 3542 0.1263 0.1773 -- 98.0
X Ray Diffraction 5.421 6.8238 -- 194 3518 0.1578 0.1957 -- 98.0
X Ray Diffraction 6.8238 38.6304 -- 182 3612 0.1526 0.1809 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.7917
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.869
f_plane_restr 0.007
f_chiral_restr 0.081
f_angle_d 1.158
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13624
Nucleic Acid Atoms 0
Heterogen Atoms 440
Solvent Atoms 720

Software

Computing
Computing Package Purpose
JDIRECTOR Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1148) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALA version: 0.1.27 data reduction