X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 303.0
Details PEG4000, 2-propanol, HEPES-Na, magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.9 α = 90
b = 139.4 β = 90
c = 100.2 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
IMAGE PLATE FUJI -- 2000-02-01
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.0 PHOTON FACTORY BL-18B

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
2.5 55.1 90.1 0.102 -- -- -- 33398 33398 0.0 0.0 14.0
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)
2.5 2.59 71.6 -- -- -- -- --

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
MOLECULAR REPLACEMENT 2.5 55.11 -- 0.0 33371 33371 1655 90.0 0.221 0.221 0.221 0.266 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 2.5 2.66 -- 231 4186 0.389 0.434 0.029 73.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 40.1
Anisotropic B[1][1] 2.98
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -16.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 13.87
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.17
c_scbond_it 1.3
c_mcangle_it 1.86
c_mcbond_it 1.05
c_improper_angle_d 0.77
c_bond_d 0.007
c_angle_deg 1.2
c_dihedral_angle_d 21.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.36
Luzzati Sigma A (Observed) 0.61
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.71
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7032
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 213

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement