X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Temperature 298.0
Details 10 mg/mL human hemoglobin, 10 mM potassium phosphate, 100 mM potassium chloride, 10-12% PEG 6000, 3 mM sodium dithionite (under anaerobic conditions), BATCH METHOD, temperature 298K, pH 7

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97 α = 90
b = 99.3 β = 90
c = 66.1 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 -- 1998-06-20
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
2.11 39.84 96.9 0.094 -- -- 6.3 37996 37996 -- -- --
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)
2.11 2.27 87.1 0.272 -- 1.5 2.6 --

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 2.11 10.0 -- 0.0 30288 30288 3440 89.73 -- 0.18648 0.18136 0.23217 matched to that in PDB id 1RQ3
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 2.1 2.152 -- 34 243 0.275 0.252 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.816
Anisotropic B[1][1] -1.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.23
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.628
r_xyhbond_nbd_refined 0.206
r_angle_other_deg 0.793
r_gen_planes_other 0.003
r_dihedral_angle_1_deg 3.651
r_gen_planes_refined 0.006
r_nbd_refined 0.247
r_symmetry_vdw_other 0.175
r_mcangle_it 1.526
r_bond_refined_d 0.022
r_symmetry_hbond_refined 0.122
r_scangle_it 3.831
r_bond_other_d 0.001
r_nbd_other 0.194
r_mcbond_it 0.801
r_dihedral_angle_3_deg 17.769
r_scbond_it 2.34
r_chiral_restr 0.094
r_xyhbond_nbd_other 0.111
r_symmetry_vdw_refined 0.055
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4384
Nucleic Acid Atoms 0
Heterogen Atoms 180
Solvent Atoms 176

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
SDMS data reduction
SDMS data scaling
X-PLOR phasing