X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details 50MM NA-CACODYLATE, PH 5.6, 10-20% PEG 400 AT ROOM TEMPERATURE. NO 2-ME ADDED. NOTE: WITH 2-ME OR LOWER PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES 1BZ4, 1OR3), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.68 α = 90
b = 55.59 β = 90
c = 63.59 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 125
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC COLLIMATOR 1997-04-15
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2.49 25 93.8 0.069 0.069 -- 6.6 5913 5913 -- 0.0 45.7
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)
2.49 2.68 82.4 0.245 0.245 4.4 4.0 --

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 2.5 10.0 -- 2.0 -- 5457 544 89.5 -- -- 0.267 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 2.5 2.59 -- 40 367 0.322 0.373 0.059 69.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 47.4
Anisotropic B[1][1] -0.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.72
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.22
x_scbond_it 2.18
x_mcangle_it 4.86
x_mcbond_it 3.31
x_improper_angle_d 1.03
x_bond_d 0.016
x_angle_deg 1.8
x_dihedral_angle_d 23.9
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.44
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.45
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1072
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 53

Software

Computing
Computing Package Purpose
UCSD Data Reduction (intensity integration)
UCSD Data Reduction (data scaling)
EPMR, X-PLOR, CCP4 Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
CCP4 model building
X-PLOR model building
EPMR model building
UCSD version: DATA REDUCTION PACKAGE data reduction
UCSD version: DATA REDUCTION PACKAGE data collection