X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 310.0
Details sodium phosphate, potassium phosphate, 1,4-butandiol, HEPES, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.9 α = 90
b = 54.9 β = 90
c = 176.8 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Supper mirror 2000-08-04
Diffraction Radiation
Monochromator Protocol
Supper mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-5 1.54180 -- --

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
1.86 15 99.9 0.079 -- -- 10.0 25165 25142 0.0 -3.0 20.4
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)
1.86 1.91 98.1 0.752 -- 3.5 8.6 --

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
Difference Fourier 1.86 15.0 0.0 0.0 -- 25152 1241 99.8 0.2 0.2 0.198 0.22 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 1.86 1.98 4011 166 4011 0.258 0.288 0.022 99.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 30.1
Anisotropic B[1][1] 3.36
Anisotropic B[1][2] 2.61
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.73
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.89
c_scbond_it 1.95
c_mcangle_it 2.52
c_mcbond_it 1.53
c_improper_angle_d 0.7
c_dihedral_angle_d 25.6
c_angle_deg 1.2
c_bond_d 0.005
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) 0.23
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2304
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 157

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS model building