X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6
Temperature 293.0
Details 390mM (NH4)2HPO4/NaH2PO4, pH 5.9-6.1, 50mM dioxane, 9-11% PEG 6,000, 15mM DTT, vapor diffusion, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 165.53 α = 90
b = 221.61 β = 99.67
c = 194.06 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
CCD MARMOSAIC 325 mm CCD -- 2010-02-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.979 SSRL BL11-1

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
3.3 50 96.5 0.114 -- -- 6.8 -- 100015 -- -- --
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)
3.3 3.42 77.6 0.847 -- -- 3.9 7978

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 3.3 49.81 -- 0.0 -- 99969 4987 -- -- 0.1929 0.1905 0.2396 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 3.29 3.38 -- 295 5061 0.2634 0.3226 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 130.557
Anisotropic B[1][1] -24.905
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 26.3277
Anisotropic B[2][2] 2.8433
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 22.0617
RMS Deviations
Key Refinement Restraint Deviation
t_angle_deg 1.21
t_bond_d 0.009
t_omega_torsion 2.37
t_other_torsion 23.17
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.883
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 28292
Nucleic Acid Atoms 373
Heterogen Atoms 9
Solvent Atoms 0

Software

Software
Software Name Purpose
BUSTER-TNT refinement version: BUSTER 2.8.0
DENZO data reduction
SCALEPACK data scaling
PDB_EXTRACT data extraction version: 3.10
BUSTER refinement version: 2.8.0