X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.9
Temperature 298.0
Details 26% PEG 4000, 7.5% glycerol, 50 mM Na Citrate pH 4.9, vapor diffusion, sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.25 α = 90
b = 104.92 β = 90
c = 125.88 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-01-14
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 0.97946 SSRL BL7-1

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
2.3 50 82.7 0.131 -- -- 5.3 52129 43111 0.0 0.0 --
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)
2.3 2.38 30.7 0.576 -- -- 2.8 1574

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
FOURIER SYNTHESIS 2.3 39.89 -- 0.0 52129 42922 2164 83.43 0.2249 0.2249 0.2229 0.2638 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 2.3 2.36 -- 55 1089 0.2608 0.2858 -- 83.43
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.5143
Anisotropic B[1][1] 6.9469
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -21.2026
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 14.2556
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 17.38
t_omega_torsion 2.63
t_bond_d 0.008
t_angle_deg 1.02
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.347
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8680
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 372

Software

Software
Software Name Purpose
SCALEPACK data scaling
BUSTER-TNT refinement
PDB_EXTRACT data extraction version: 3.11
Blu-Ice data collection
HKL-2000 data reduction
BUSTER phasing
BUSTER refinement version: 2.11.4