X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 293.0
Details VAPOR DIFFUSION BY HANGING DROPS. 0.1 M SODIUM ACETATE, 20% ETHANOL, 1:1 WITH WATER SOLUTION OF THE PROTEIN (30 MG/ML)., pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.96 α = 90
b = 51.43 β = 90
c = 128.9 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR SIEMENS-NICOLET X100 monochromator 1994-06-27
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE SIEMENS 1.5418 -- --

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 30 93.0 0.07 0.07 -- 3.5 110551 99496 2.0 1.36 14.7

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 1.8 27.52 1.36 2.0 29883 29319 1441 92.7 0.171 0.1675 0.1647 0.193 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 1.8 1.85 1949 122 1949 0.188 0.218 0.02 80.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 19.9
Anisotropic B[1][1] 2.66
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.57
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.005
c_mcangle_it 2.05
c_scangle_it 3.11
c_mcbond_it 1.27
c_improper_angle_d 0.72
c_dihedral_angle_d 26.2
c_angle_deg 1.3
c_scbond_it 2.11
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.17
Luzzati Sigma A (Observed) 0.08
Luzzati Resolution Cutoff (Low) 30.0
Luzzati ESD (R-Free Set) 0.2
Luzzati Sigma A (R-Free Set) 0.1
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2560
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 249

Software

Software
Software Name Purpose
Frambo data collection
SAINT data reduction
AMoRE phasing
CNS refinement version: 1.0
FRAMBO data reduction
SAINT data scaling