X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details 500 mM Sodium acetate, 50 mM HEPES, 25 mM Cadmium sulfate , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 187.09 α = 90
b = 187.09 β = 90
c = 116 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Double focussing x-ray optics 2000-03-12
Diffraction Radiation
Monochromator Protocol
double crystal monochromator, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.042 MPG/DESY, HAMBURG BW6

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
1.95 20 98.3 -- 0.051 -- 3.8 55756 55315 0.0 2.0 19.8
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)
1.95 2.07 98.6 -- 0.28 2.7 3.7 8767

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 1.95 19.68 0.0 0.0 55315 55315 2835 98.1 0.196 0.196 0.196 0.231 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 1.95 2.07 8767 449 8767 0.244 0.279 0.013 98.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 35.4
Anisotropic B[1][1] -2.39
Anisotropic B[1][2] -0.09
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.78
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.01
c_angle_deg 1.5
c_improper_angle_d 0.96
c_scbond_it 2.15
c_dihedral_angle_d 23.6
c_mcbond_it 1.39
c_scangle_it 3.06
c_mcangle_it 2.08
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.18
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4077
Nucleic Acid Atoms 0
Heterogen Atoms 73
Solvent Atoms 566

Software

Software
Software Name Purpose
CCP4 model building
CNS refinement version: 1.0
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
CCP4 phasing