X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.2
Temperature 296.0
Details PEG 550, magnesium acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 269.24 α = 90
b = 269.24 β = 90
c = 638.14 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-09-28
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1.15 ALS 5.0.2

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
3.4 39.79 86.1 -- 0.17 -- 12.1 203504 203504 0.0 0.0 --
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)
3.4 3.46 55.4 -- -- 0.58 1.34 610

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 3.4 39.7 -- 4.0 203504 102537 5118 50.3 0.428 0.24 0.238 0.25 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 3.4 3.52 616 28 376 0.4154 0.3987 0.075 1.7
X Ray Diffraction 3.56 3.74 2348 121 2227 0.338 0.364 0.033 7.9
X Ray Diffraction 3.74 3.98 5780 308 5472 0.311 0.293 0.017 19.5
X Ray Diffraction 3.98 4.28 9259 426 8833 0.288 0.296 0.014 31.2
X Ray Diffraction 4.28 4.71 17014 874 16140 0.265 0.276 0.009 57.4
X Ray Diffraction 4.71 5.39 19840 991 18849 0.245 0.268 0.009 67.0
X Ray Diffraction 5.39 6.79 22258 1114 21144 0.235 0.244 0.007 75.2
X Ray Diffraction 6.79 39.79 25313 1243 24070 0.218 0.225 0.006 85.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Restrained
Mean Isotropic B 102.3
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 46.89
x_scbond_it 33.96
x_mcangle_it 19.98
x_mcbond_it 13.37
x_improper_angle_d 0.69
x_dihedral_angle_d 29.7
x_angle_deg 1.5
x_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.54
Luzzati Sigma A (Observed) 0.8
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.56
Luzzati Sigma A (R-Free Set) 1.08
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3741
Nucleic Acid Atoms 0
Heterogen Atoms 21
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.1 refinement