X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Liquid Liquid Diffusion
pH 7.5
Details PROTEIN WAS CRYSTALLIZED BY LIQUID-LIQUID DIFFUSION METHOD. PRECIPITANT CONTAINED 5-15% GLYCEROL, 18.75-22.5% PEG 4000, 230-270 MM CACL2, AND 50 MM HEPES PH 7.5. PROTEIN WAS STORED BEFORE CRYSTALLIZATION IN 20% GLYCEROL, 50 MM HEPES, PH 7.5, AND 2 MM NA2S2O4., liquid - liquid diffusion

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.6 α = 90
b = 75.87 β = 114.17
c = 53.55 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC -- 1993-11
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU -- -- --

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
1.93 15.63 98.8 0.0725 -- -- 6.8 -- 36808 -- 0.0 34.5
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)
1.93 2.0 91.0 -- -- -- -- --

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 1.93 5.0 -- 0.0 -- 31231 3083 98.8 -- 0.209 0.209 0.297 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 1.93 2.0 -- 311 2808 0.343 0.385 0.022 99.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.3
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.89
x_bond_d 0.018
x_angle_deg 2.0
x_dihedral_angle_d 24.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Resolution Cutoff (Low) 5.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4080
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 118

Software

Computing
Computing Package Purpose
R-AXIS IIC Data Reduction (intensity integration)
REFSTAT Data Reduction (data scaling)
X-PLOR 3.1 Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
X-PLOR version: 3.1 model building