X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details PROTEIN WAS CRYSTALLIZED FROM 18% PEG 6000, 53 MM MGCL2, 2MM MGADP-, 25 MM KNO3, 10 MM ARGININE 0.5 MM DTT, 2.5 MM SODIUM AZIDE, 25 MM HEPES, PH 7.5, WITH 20 MG/ML OF PROTEIN CONCENTRATION.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.44 α = 90
b = 70.89 β = 90
c = 80.44 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 RIGAKU RAXIS IIC GRAPHITE MONOCHROMATOR OPTICS 1996-09-13
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
1.86 35 98.9 0.047 -- -- 6.7 -- 34737 -- 1.0 16.8
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)
1.86 1.94 98.5 0.157 -- -- -- --

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, MIR 1.86 5.0 -- 2.0 -- 29223 -- 98.9 -- 0.196 0.196 0.224 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 1.86 1.94 -- -- 3314 0.236 0.255 -- 98.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GAUSSIAN DISTRIBUTION
Mean Isotropic B 16.6
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 2.803
x_scbond_it 1.83
x_mcangle_it 1.449
x_mcbond_it 0.945
x_improper_angle_d 1.15
x_bond_d 0.013
x_angle_deg 1.94
x_dihedral_angle_d 22.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.237
Luzzati Sigma A (R-Free Set) 0.15
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2817
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 298

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.8 Structure Solution
X-PLOR 3.8 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.8 refinement
X-PLOR version: 3.8 model building