X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.8
Details PROTEIN WAS CRYSTALLIZED BY MIXING WITH EQUAL VOLUME OF 60% AMMONIUM SULPHATE IN 20 MM TRI-HCL BUFFER AT PH 7.8 CONTAINING AND AT ROOM TEMPERATURE

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.57 α = 90
b = 56.79 β = 95.8
c = 39.62 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU -- 1995-06-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A -- PHOTON FACTORY BL-6A

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
2.6 100 90.0 0.102 -- -- 4.1 -- 7253 -- 3.0 25.1
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)
2.6 2.72 74.0 0.145 -- 8.6 2.3 --

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
SIRAS 2.6 6.0 -- 2.0 -- 6570 367 88.8 -- 0.182 0.182 0.271 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 2.6 2.75 -- 53 842 0.234 0.33 0.045 73.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 17.3
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 3.0
x_scbond_it 2.13
x_mcangle_it 2.16
x_mcbond_it 1.44
x_improper_angle_d 1.51
x_bond_d 0.013
x_angle_deg 1.8
x_dihedral_angle_d 25.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.3
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.35
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2047
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 83

Software

Computing
Computing Package Purpose
WEIS, DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASES Structure Solution
X-PLOR 2.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 2.1 refinement
PHASES version: PROGRAM PACKAGE model building
SCALEPACK data reduction
DENZO data collection
WEIS data collection