X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details Protein Solution (20 mg/ml myoglobin, 60% saturated ammonium sulfate, 20 mM Tris, pH 7.5, 5 mM sodium azide, 1 mM EDTA); Well Solution (65% saturated ammonium sulfate, 20 mM Tris, pH 7.5, 1 mM EDTA); Cryoprotectant (68% ammonium sulfate, 20 mM Tris, pH 7.5, 5 mM EDTA, 20% glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.35 α = 90
b = 28.78 β = 106.07
c = 63.04 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD 20-micron minibeam collimator used 2009-08-14
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B

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
1.5 50 97.7 0.068 0.068 -- 4.9 19856 19856 0.0 0.0 15.6
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)
1.5 1.55 91.4 0.299 0.299 5.06 3.8 --

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
FOURIER SYNTHESIS 1.5 33.9 -- 0.0 18880 18880 914 95.0 0.182 0.181 0.181 0.212 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 1.5 1.59 2630 133 2630 0.21 0.222 0.019 84.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 16.3
Anisotropic B[1][1] 2.51
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.78
Anisotropic B[2][2] 2.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.83
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.81
c_scbond_it 1.92
c_mcangle_it 1.32
c_mcbond_it 0.91
c_improper_angle_d 0.71
c_bond_d 0.005
c_angle_deg 1.0
c_dihedral_angle_d 16.6
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.15
Luzzati Sigma A (Observed) 0.08
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.19
Luzzati Sigma A (R-Free Set) 0.08
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1195
Nucleic Acid Atoms 0
Heterogen Atoms 58
Solvent Atoms 115

Software

Computing
Computing Package Purpose
JBluice Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
CNS 1.3 Structure Refinement
Software
Software Name Purpose
CNS version: 1.3 refinement
CNS model building
JBluice data collection