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 6.0, 50mM dioxane, 9-11% PEG 6,000, 15mM DTT, vapor diffusion, temperature 293K, VAPOR DIFFUSION

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 157.54 α = 90
b = 221.27 β = 97.44
c = 192.18 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
IMAGE PLATE MAR scanner 300 mm plate -- 2010-01-01
Diffraction Radiation
Monochromator Protocol
Double crystal cryo-cooled SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.979 APS 23-ID-D

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 99.4 0.173 -- -- 3.8 -- 97374 -- -- --
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 3.36 99.2 0.769 -- -- 3.8 4848

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 45.14 -- 0.0 -- 97341 4848 -- -- 0.1897 0.1875 0.2304 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 -- 357 6153 0.2342 0.2668 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 95.0929
Anisotropic B[1][1] -34.9796
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 20.7697
Anisotropic B[2][2] 11.1185
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 23.8612
RMS Deviations
Key Refinement Restraint Deviation
t_angle_deg 1.14
t_omega_torsion 2.26
t_other_torsion 22.91
t_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.674
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 28292
Nucleic Acid Atoms 269
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