X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 4.0 AMMONIUM FORMATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 205.6 α = 90
b = 205.6 β = 90
c = 56.42 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-11-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.9800 NSLS X9B

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
2.8 25 95.4 0.062 -- -- 7.8 17298 17298 0.0 0.0 44.6
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)
2.79 2.9 98.0 0.328 -- -- 7.6 1938

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 2.8 24.73 0.0 0.0 16517 16517 643 92.8 -- 0.248 0.248 0.296 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 2.8 2.98 -- 107 2596 0.413 0.428 0.041 93.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 75.4
Anisotropic B[1][1] 7.94
Anisotropic B[1][2] 7.66
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.94
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -15.88
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 10.81
c_scbond_it 7.68
c_mcangle_it 9.37
c_mcbond_it 6.13
c_improper_angle_d 1.04
c_bond_d 0.019
c_angle_deg 2.1
c_dihedral_angle_d 28.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.45
Luzzati Sigma A (Observed) 0.76
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.54
Luzzati Sigma A (R-Free Set) 0.72
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2436
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 91

Software

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