X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 277.0
Details 20.0% 1,3-butanediol, 0.1M sodium acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.54 α = 90
b = 143.31 β = 94.35
c = 67.56 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
PIXEL DECTRIS PILATUS 6M Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator 2012-03-11
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 -- SSRL BL12-2

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
2.25 29.68 97.5 0.078 -- -- -- -- 52331 -- -3.0 48.088
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)
2.25 2.33 94.7 0.889 -- 1.4 -- --

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
SAD 2.25 29.682 -- 0.0 -- 52298 2656 97.91 -- 0.1711 0.1689 0.213 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 2.25 2.31 -- 192 3488 0.2432 0.2995 -- 97.91
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.0499
Anisotropic B[1][1] 1.6031
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.5626
Anisotropic B[2][2] 0.777
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.3801
RMS Deviations
Key Refinement Restraint Deviation
t_bond_d 0.01
t_angle_deg 1.13
t_omega_torsion 3.66
t_other_torsion 2.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.282
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7049
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 569

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling version: December 29, 2011
BUSTER-TNT refinement version: 2.10.0
XDS data reduction
SHELXD phasing
BUSTER refinement version: 2.10.0