X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch
pH 7
Temperature 298.0
Details 10% PEG 6000, 10 mM potassium phosphate, 100 mM potassium chloride, 3 mM sodium dithionite, 10 mg/ml Hb, pH 7.0, batch, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.3 α = 90
b = 99.4 β = 90
c = 65.9 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR SDMS GRAPHITE 1996-01-24
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

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
2.12 50 97.9 0.078 -- -- 6.6 36200 36200 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)
2.12 2.28 89.4 0.243 -- 2.2 3.1 6518

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 2.12 10.0 -- 2.0 35347 33773 3010 97.9 -- -- 0.176 0.244 MATCHED TO PDB ENTRY 1Y0T
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 2.12 2.28 5527 451 -- 0.243 0.287 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 23.79
RMS Deviations
Key Refinement Restraint Deviation
p_planar_d 0.04
p_bond_d 0.01
p_xyhbond_nbd 0.175
p_scangle_it 6.906
p_multtor_nbd 0.171
p_transverse_tor 32.2
p_singtor_nbd 0.164
p_chiral_restr 0.133
p_staggered_tor 20.5
p_scbond_it 5.317
p_plane_restr 0.01
p_planar_tor 2.3
p_mcangle_it 3.317
p_mcbond_it 2.404
p_angle_d 0.025
p_hb_or_metal_coord 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4384
Nucleic Acid Atoms 0
Heterogen Atoms 172
Solvent Atoms 194

Software

Software
Software Name Purpose
SDMS data collection
SDMS data reduction
X-PLOR model building
PROLSQ refinement
SDMS data scaling
X-PLOR phasing