X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 296.0
Details PEG-monomethyl ether 5000, sodium cacodylate, ammonium sulfate, KCL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.14 α = 71.67
b = 69.63 β = 85.72
c = 73.96 γ = 75.11
Symmetry
Space Group P 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 1997-09-02
IMAGE PLATE RIGAKU RAXIS IV -- 1997-09-01
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.54178 -- --

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
2.8 23 88.0 0.138 -- -- 1.9 24659 24659 0.0 -3.0 41.9
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)
2.8 2.88 74.0 0.333 -- 2.0 -- --

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
MOLECULAR REPLACEMENT 2.89 22.95 -- 0.0 23376 23376 2315 83.8 -- 0.239 0.236 0.264 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 2.89 3.07 -- 323 2826 0.324 0.316 0.018 67.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 23.8
Anisotropic B[1][1] 1.65
Anisotropic B[1][2] -1.99
Anisotropic B[1][3] 6.33
Anisotropic B[2][2] -4.36
Anisotropic B[2][3] -1.09
Anisotropic B[3][3] 2.71
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.83
c_dihedral_angle_d 23.3
c_angle_deg 1.5
c_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.52
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9236
Nucleic Acid Atoms 0
Heterogen Atoms 209
Solvent Atoms 48

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