X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 277.0
Details 2.40M ammonium sulfate, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.01 α = 90
b = 66.01 β = 90
c = 263.46 γ = 90
Symmetry
Space Group P 41 2 2

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 2012-05-31
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795,0.9184 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
2.48 46.68 99.6 0.072 -- -- -- -- 21701 -- -3.0 76.09
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)
2.48 2.57 99.8 1.17 -- 1.7 -- --

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
MAD 2.48 46.676 -- 0.0 -- 21634 1106 99.67 -- 0.1983 0.1969 0.2251 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 2.48 2.6 -- 151 2641 0.23 0.2816 -- 99.67
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 76.5292
Anisotropic B[1][1] -2.5059
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.5059
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.0117
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 2.13
t_omega_torsion 3.58
t_angle_deg 1.09
t_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.467
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2933
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 72

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SHELXD,SHARP Structure Solution
BUSTER 2.10.0 Structure Refinement
Software
Software Name Purpose
BUSTER-TNT version: 2.10.0 refinement
Xscale version: March 15, 2012 data processing
SHARP phasing
SHELX phasing
pdb_extract version: 3.10 data extraction
MOLPROBITY version: 3beta29 validation