X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.4
Temperature 290.0
Details K/Na phosphate, MPD , pH 6.40, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.31 α = 90
b = 87.35 β = 90
c = 45.17 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID -- APS 19-ID

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
1.8 19.9 93.8 0.074 -- -- 4.2 47714 47714 -- 2.4 16.0
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 1.82 95.4 0.494 -- 2.4 4.1 1601

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
CNS, done by rigid body refinement of starting model. 1.8 19.9 0.0 0.0 -- 45593 3473 89.5 -- 0.197 0.197 0.211 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 1.8 1.91 -- 558 6525 0.245 0.258 0.011 85.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 26.2
Anisotropic B[1][1] -1.53
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.98
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.44
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.2
c_bond_d 0.008
c_mcbond_it 0.95
c_dihedral_angle_d 25.5
c_scbond_it 1.56
c_scangle_it 2.48
c_angle_deg 1.5
c_mcangle_it 1.57
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
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) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3118
Nucleic Acid Atoms 0
Heterogen Atoms 67
Solvent Atoms 352

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
CNS phasing