X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details 1.9M Sodium Malonate, pH 7.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.09 α = 90
b = 89.09 β = 90
c = 163.62 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 8-BM -- APS 8-BM

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 50 90.0 -- 0.078 -- 5.2 -- 40511 -- -- 19.9
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)
2.0 2.07 91.7 -- 0.293 3.8 -- --

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 2.0 49.91 -- 0.0 40511 39099 1947 86.9 -- 0.278 0.278 0.325 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 2.0 2.13 -- 302 5736 0.33 0.364 0.021 81.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 39.2
Anisotropic B[1][1] 4.48
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.48
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.95
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 3.62
c_bond_d 0.006
c_scbond_it 4.97
c_scangle_it 6.22
c_angle_deg 1.4
c_mcangle_it 4.59
c_dihedral_angle_d 24.1
c_improper_angle_d 0.82
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.4
Luzzati Sigma A (R-Free Set) 0.29
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2709
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 178

Software

Software
Software Name Purpose
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
EPMR phasing