X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 0.1 M Imidazole, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.15 α = 90
b = 78.96 β = 99.67
c = 69.24 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-08-08
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
1.43 28.97 96.6 -- 0.039 -- 3.83 123161 123161 -3.0 -3.0 15.3
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)
1.43 1.47 94.1 -- 0.653 2.16 3.55 8862

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 1.43 28.971 -- 0.0 123157 123157 6168 96.63 -- 0.1778 0.1773 0.1884 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 1.43 1.4463 3823 172 3823 0.3247 0.3297 -- 94.0
X Ray Diffraction 1.4463 1.4633 3778 216 3778 0.2935 0.3109 -- 95.0
X Ray Diffraction 1.4633 1.4811 3789 219 3789 0.2719 0.3125 -- 95.0
X Ray Diffraction 1.4811 1.4999 3770 217 3770 0.2576 0.2829 -- 95.0
X Ray Diffraction 1.4999 1.5196 3840 206 3840 0.2502 0.2506 -- 95.0
X Ray Diffraction 1.5196 1.5404 3820 200 3820 0.2358 0.2487 -- 95.0
X Ray Diffraction 1.5404 1.5624 3821 195 3821 0.2232 0.2471 -- 95.0
X Ray Diffraction 1.5624 1.5857 3880 187 3880 0.2133 0.2176 -- 95.0
X Ray Diffraction 1.5857 1.6105 3847 215 3847 0.2161 0.2639 -- 96.0
X Ray Diffraction 1.6105 1.6369 3802 215 3802 0.2144 0.2731 -- 95.0
X Ray Diffraction 1.6369 1.6651 3862 219 3862 0.2116 0.2156 -- 96.0
X Ray Diffraction 1.6651 1.6954 3859 217 3859 0.2047 0.2395 -- 96.0
X Ray Diffraction 1.6954 1.728 3917 180 3917 0.1918 0.1977 -- 96.0
X Ray Diffraction 1.728 1.7633 3835 201 3835 0.1861 0.197 -- 96.0
X Ray Diffraction 1.7633 1.8016 3920 214 3920 0.172 0.2132 -- 97.0
X Ray Diffraction 1.8016 1.8435 3847 205 3847 0.1674 0.1638 -- 97.0
X Ray Diffraction 1.8435 1.8896 3919 204 3919 0.1697 0.1686 -- 97.0
X Ray Diffraction 1.8896 1.9407 3894 232 3894 0.1702 0.1983 -- 97.0
X Ray Diffraction 1.9407 1.9978 3901 199 3901 0.1673 0.1751 -- 97.0
X Ray Diffraction 1.9978 2.0623 3958 198 3958 0.1707 0.1781 -- 97.0
X Ray Diffraction 2.0623 2.1359 3976 181 3976 0.1685 0.1858 -- 98.0
X Ray Diffraction 2.1359 2.2214 3925 211 3925 0.1726 0.1755 -- 98.0
X Ray Diffraction 2.2214 2.3225 3975 223 3975 0.167 0.1589 -- 98.0
X Ray Diffraction 2.3225 2.4449 3935 216 3935 0.1617 0.1819 -- 98.0
X Ray Diffraction 2.4449 2.598 3955 199 3955 0.1677 0.1697 -- 98.0
X Ray Diffraction 2.598 2.7984 3985 215 3985 0.1745 0.1861 -- 98.0
X Ray Diffraction 2.7984 3.0797 4002 195 4002 0.1724 0.188 -- 98.0
X Ray Diffraction 3.0797 3.5247 4012 190 4012 0.1641 0.1768 -- 98.0
X Ray Diffraction 3.5247 4.4382 4022 224 4022 0.1471 0.1478 -- 99.0
X Ray Diffraction 4.4382 28.9765 4120 203 4120 0.1694 0.1771 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic, TLS
Mean Isotropic B 21.768
Anisotropic B[1][1] -1.0584
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.47
Anisotropic B[2][2] -1.8628
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.9211
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.067
f_dihedral_angle_d 12.004
f_angle_d 0.984
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4829
Nucleic Acid Atoms 0
Heterogen Atoms 84
Solvent Atoms 753

Software

Computing
Computing Package Purpose
SERGUI Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER (2.1.4) Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
PHASER version: (2.1.4) model building
SERGUI data collection