X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 292.0
Details 0.1 M lithium sulfate, 0.1 M MES, 20% PEG mme 2000, 0.15 M glycine , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.54 α = 90
b = 93.65 β = 90
c = 116.89 γ = 90
Symmetry
Space Group P 2 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 -- 2011-10-22
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 0.918 CHESS F1

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
2.8 40 99.9 0.132 0.132 -- 13.9 14238 14187 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)
2.8 2.85 100.0 0.0 0.0 2.306 14.1 --

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 2.8163 38.655 -- 1.34 14238 14187 1418 99.3 -- 0.2345 0.2295 0.2767 random using lattice symmetry
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 2.8163 2.9169 -- 135 1209 0.3358 0.3715 -- 97.0
X Ray Diffraction 2.9169 3.0337 -- 142 1280 0.2997 0.3434 -- 100.0
X Ray Diffraction 3.0337 3.1717 -- 138 1240 0.2942 0.3592 -- 100.0
X Ray Diffraction 3.1717 3.3388 -- 141 1276 0.2755 0.3397 -- 100.0
X Ray Diffraction 3.3388 3.5479 -- 140 1257 0.2665 0.2964 -- 100.0
X Ray Diffraction 3.5479 3.8216 -- 139 1255 0.2341 0.2799 -- 99.0
X Ray Diffraction 3.8216 4.2057 -- 140 1273 0.2223 0.2897 -- 99.0
X Ray Diffraction 4.2057 4.8133 -- 144 1293 0.1829 0.2367 -- 100.0
X Ray Diffraction 4.8133 6.0605 -- 146 1312 0.2168 0.2527 -- 100.0
X Ray Diffraction 6.0605 38.6587 -- 153 1374 0.206 0.2473 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 93.5261
Anisotropic B[1][1] -6.3956
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.4884
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.9071
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 7.851
f_plane_restr 0.002
f_chiral_restr 0.035
f_angle_d 0.499
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3385
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 24

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1012) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 2.5.0 molecular replacement
HKL data reduction