X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 33% (w/v) PEG 2000 MME, 0.1M Na-HEPES (pH 7.0), vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.57 α = 90
b = 81.03 β = 90.13
c = 68.62 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 ADSC QUANTUM 270 mirrors 2009-05-20
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A

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
1.35 23.51 91.5 -- 0.048 -- 3.5 145439 145439 -- -- 16.93
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)
1.35 1.39 56.2 0.725 0.725 1.1 2.3 6593

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 1.351 19.77 -- 0.0 -- 145392 7284 91.18 -- 0.1761 0.175 0.1968 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 1.35 1.39 -- 307 6092 0.2409 0.257 -- 91.18
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.9248
Anisotropic B[1][1] 1.3338
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.5381
Anisotropic B[2][2] -3.3685
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.0347
RMS Deviations
Key Refinement Restraint Deviation
t_bond_d 0.01
t_other_torsion 16.32
t_omega_torsion 4.13
t_angle_deg 1.07
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.155
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5620
Nucleic Acid Atoms 0
Heterogen Atoms 149
Solvent Atoms 959

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.9
PHASER phasing version: 2.1.4
BUSTER-TNT refinement version: BUSTER 2.11.2
PDB_EXTRACT data extraction version: 3.11
XDS data reduction
BUSTER refinement version: 2.11.2