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 = 57.66 α = 90
b = 85.61 β = 93.25
c = 115.23 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2006-09-01
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
2.2 50 84.8 0.116 -- -- 3.0 56942 48287 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)
2.2 2.28 50.1 0.321 -- -- 1.8 2825

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 2.2 40.12 -- 0.0 56942 48259 2446 84.81 0.1942 0.1942 0.1918 0.2406 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 2.26 -- 101 1914 0.2421 0.2526 -- 84.81
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.4056
Anisotropic B[1][1] -8.7073
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.3093
Anisotropic B[2][2] 4.5391
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.1682
RMS Deviations
Key Refinement Restraint Deviation
t_angle_deg 1.05
t_other_torsion 16.68
t_bond_d 0.009
t_omega_torsion 3.11
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.262
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8680
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 589

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