X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion/hanging Drop
pH 5
Temperature 298.0
Details ammonium sulfate, sodium citrate, pH 5.0, vapor diffusion/hanging drop, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.6 α = 90
b = 67.4 β = 90
c = 87.3 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE WEISSENBERG -- 1999-05-25
Diffraction Radiation
Monochromator Protocol
SI (1 1 1) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B -- PHOTON FACTORY BL-6B

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
1.8 20 85.5 0.035 -- -- 3.1 -- 31955 -- -- 16.9
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)
1.8 1.85 71.5 0.489 -- -- 2.7 1939

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
MR 1.9 20.0 -- 2.0 -- 27784 2712 86.6 -- 0.199 0.199 0.24 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 1.9 2.02 -- 382 3455 0.24 0.27 0.014 73.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 24.8
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 3.98
x_scbond_it 2.91
x_mcangle_it 2.03
x_mcbond_it 1.54
x_improper_angle_d 0.85
x_dihedral_angle_d 26.0
x_angle_deg 1.6
x_bond_d 0.014
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.25
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2672
Nucleic Acid Atoms 0
Heterogen Atoms 140
Solvent Atoms 137

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 Data Reduction (data scaling)
X-PLOR 98.1 Structure Solution
X-PLOR 98.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 98.1 refinement
X-PLOR version: 98.1 model building