X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 291.0
Details 1.8M sodium malonate pH 5.0, 0.1M sodium acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 147.99 α = 90
b = 147.99 β = 90
c = 33.71 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- --
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1.00000, 0.97937, 0.97918, 0.95370 ALS 5.0.2

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
1.87 46.8 -- -- -- -- 97.6 -- 33679 -- -- 17.4
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)
1.8 1.86 -- -- -- 1.58 80.7 2764

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 1.9 46.8 -- -- 30763 30635 1828 99.6 -- -- 0.18 0.21 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 1.87 1.96 3488 210 -- 0.252 0.296 0.02 98.1
X Ray Diffraction 1.96 2.06 3766 237 -- 0.203 0.252 0.016 98.8
X Ray Diffraction 2.06 2.19 3779 224 -- 0.188 0.241 0.016 99.4
X Ray Diffraction 2.19 2.36 3823 231 -- 0.165 0.193 0.013 99.5
X Ray Diffraction 2.36 2.59 3860 243 -- 0.175 0.229 0.015 99.8
X Ray Diffraction 2.59 2.97 3824 223 -- 0.177 0.224 0.015 99.8
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.29
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.58
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 1.58
c_mcbond_it 0.012
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.17
Luzzati Sigma A (Observed) 0.15
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2478
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 184

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
SOLVE phasing
CNS refinement version: 1.0
HKL-2000 data reduction