X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details PEG 400; NaCl; Bis-Tris Propane; CoCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.8 α = 90
b = 104.8 β = 90
c = 104.2 γ = 120
Symmetry
Space Group P 64

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 140
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 KOHZU double crystal monochromator 2000-03-15
Diffraction Radiation
Monochromator Protocol
KOHZU double crystal monochormator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 1.5418 NSLS X4A

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 20 99.5 -- 7.4 -- 11.46 43331 43331 0.0 0.0 27.1
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 96.2 -- 56.7 6.58 2.14 3595

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
MIR 2.0 20.0 0.0 2.0 43331 40380 4029 92.2 -- -- 0.233 0.263 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 -- 585 5087 0.365 0.376 0.016 78.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 41.6
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 5.72
x_scbond_it 3.57
x_mcangle_it 3.47
x_mcbond_it 2.08
x_improper_angle_d 1.23
x_dihedral_angle_d 20.5
x_angle_deg 1.1
x_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.34
Luzzati Sigma A (Observed) 0.41
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1447
Nucleic Acid Atoms 1300
Heterogen Atoms 6
Solvent Atoms 227

Software

Computing
Computing Package Purpose
IN-HOUSE SOFTWARE AT NSLS Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MLPHARE Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR(ONLINE) version: 3.851 refinement
MLPHARE model building