X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 10.6
Temperature 293.0
Details 1.5M Sodium/Potassium Phosphate, 200mM Lithium Sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.3 α = 90
b = 125.3 β = 90
c = 64.6 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 ADSC QUANTUM 4 -- 2001-06-01
Diffraction Radiation
Monochromator Protocol
Focused Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.97900, 0.97938, 0.95369 NSLS X9B

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
2.4 99 99.5 0.096 -- -- 10.3 34965 34790 5.0 5.0 --
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)
2.4 2.49 99.3 0.303 -- 6.7 -- 3381

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 2.4 35.08 -- 0.0 62036 62036 6184 93.5 -- -- 0.213 0.257 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 2.4 2.55 9302 914 8388 0.263 0.309 0.01 84.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 38.6
Anisotropic B[1][1] -8.29
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.18
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 19.7
c_mcangle_it 2.3
c_scangle_it 3.47
c_bond_d 0.007
c_mcbond_it 1.37
c_improper_angle_d 0.87
c_scbond_it 2.29
c_angle_deg 1.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.28
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.36
Luzzati Sigma A (R-Free Set) 0.34
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5418
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 237

Software

Software
Software Name Purpose
SOLVE phasing
RESOLVE model building
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
RESOLVE phasing