X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Details CRYSTALLIZED IN HANGING DROPS CONTAINING PROTEIN MIXED 1:1 WITH WELL SOLUTION OF 7.2-7.5% PEG 8000, 500MM NACL AND 100 MM PHOSPHATE BUFFER (PH 5.4-5.6), VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.4 α = 90
b = 134.2 β = 90
c = 71.6 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1998-08-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F2 -- CHESS F2

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
3 40 92.4 -- 0.137 -- 3.5 -- 21547 -- -3.0 --
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)
3.0 3.16 93.9 -- 0.527 2.6 3.5 --

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 3.0 15.0 -- 0.0 21016 21016 2089 90.1 -- -- 0.203 0.262 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 3.0 3.11 -- 211 1735 0.296 0.389 0.027 84.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 36.0
Anisotropic B[1][1] -14.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -22.7
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 36.92
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 23.3
c_scbond_it 1.96
c_bond_d 0.008
c_mcangle_it 6.77
c_scangle_it 3.41
c_angle_deg 1.2
c_mcbond_it 4.3
c_improper_angle_d 1.74
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.43
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.54
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5633
Nucleic Acid Atoms 0
Heterogen Atoms 107
Solvent Atoms 46

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 0.5
MOSFLM data reduction
CCP4 data scaling version: (SCALA)