X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 289.0
Details 0.1M Tris, pH 8.0, 2M sodium chloride, 4% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.2 α = 90
b = 63.2 β = 90
c = 249.26 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2003-07-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID

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 50 99.9 0.123 -- -- -- 19497 19421 2.0 1.7 --
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 2.59 99.8 0.994 -- -- -- 1921

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 2.5 45.71 -- 0.0 19497 19421 1033 99.9 0.235 0.235 0.233 0.271 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 2.65 3221 162 3059 0.298 0.33 0.026 99.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 53.6
Anisotropic B[1][1] 2.2
Anisotropic B[1][2] 1.19
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.41
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.01
c_mcbond_it 1.39
c_angle_deg 1.3
c_mcangle_it 2.39
c_improper_angle_d 0.89
c_scangle_it 3.65
c_scbond_it 2.36
c_dihedral_angle_d 18.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.34
Luzzati Sigma A (Observed) 0.37
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.41
Luzzati Sigma A (R-Free Set) 0.43
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3473
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 17

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
PDB_EXTRACT data extraction version: 2.000
ADSC data collection version: QUANTUM
HKL-2000 data reduction
AMoRE phasing
CNX refinement version: 2002