X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 298.0
Details PEGMME 2000, sodium acetate, ammonium sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.25 α = 90
b = 51.25 β = 90
c = 59.87 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-01-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B 0.9795 NSLS X12B

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 50 99.6 0.035 -- -- 3.8 40929 5440 0.0 0.0 19.1
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)
1.8 1.86 99.1 0.104 -- 11.1 3.4 538

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 24.82 0.0 0.0 5439 5439 580 99.7 -- 0.179 0.179 0.222 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 1.86 493 50 443 0.221 0.273 0.039 99.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 19.8
Anisotropic B[1][1] 0.31
Anisotropic B[1][2] 0.66
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.62
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.008
c_dihedral_angle_d 14.8
c_improper_angle_d 0.65
c_mcangle_it 1.72
c_angle_deg 1.0
c_scbond_it 2.34
c_mcbond_it 1.23
c_scangle_it 3.37
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.17
Luzzati Sigma A (Observed) 0.1
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 489
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 83

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
AMORE model building
CNS version: 1.0 refinement