X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 0.1M Tris-HCl, pH 7.0-8.0, 3.5 - 4.0 ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 206.62 α = 90
b = 206.62 β = 90
c = 56.17 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 -- 1999-01-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.97178 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
2.5 15 98.5 0.097 -- -- 5.86 24873 24873 0.0 0.0 36.5
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)
2.5 2.53 85.5 0.431 -- -- 3.54 1051

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
MIR 2.5 14.96 -- 2.0 -- 22664 862 91.2 -- 0.243 0.243 0.299 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 2.66 -- 107 2945 0.402 0.399 0.039 75.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 65.8
Anisotropic B[1][1] 5.6
Anisotropic B[1][2] 5.03
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.2
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 10.55
c_mcbond_it 7.17
c_scbond_it 9.45
c_dihedral_angle_d 26.6
c_bond_d 0.018
c_scangle_it 12.65
c_angle_deg 2.0
c_improper_angle_d 1.18
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.43
Luzzati Sigma A (Observed) 0.66
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.52
Luzzati Sigma A (R-Free Set) 0.67
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2506
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 82

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE, ROTPTF V. 6D Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
SCALEPACK data reduction
Rotptf_6D model building
DENZO data collection
SOLVE model building
CNS version: 1.0 refinement