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 = 96.8 α = 90
b = 98.6 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 GRAPHITE --
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
2.1 50 -- -- -- -- -- -- n/a -- 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)
2.1 2.29 87.6 -- -- -- -- --

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 2.1 10.0 -- 0.0 -- 32012 3484 95.38 -- 0.19587 0.19122 0.23777 10 SETS MATCHED TO PDB ENTRY 1Y0W
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 2.29 -- 625 6410 0.258 0.317 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.996
Anisotropic B[1][1] 0.44
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.49
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.872
r_symmetry_vdw_other 0.302
r_gen_planes_refined 0.007
r_symmetry_vdw_refined 0.146
r_bond_refined_d 0.019
r_dihedral_angle_3_deg 17.384
r_mcangle_it 1.477
r_scbond_it 2.423
r_dihedral_angle_1_deg 3.61
r_xyhbond_nbd_other 0.04
r_angle_other_deg 1.194
r_symmetry_hbond_refined 0.202
r_xyhbond_nbd_refined 0.221
r_nbd_other 0.207
r_scangle_it 3.853
r_chiral_restr 0.103
r_mcbond_it 0.79
r_gen_planes_other 0.006
r_nbd_refined 0.242
r_bond_other_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4378
Nucleic Acid Atoms 0
Heterogen Atoms 172
Solvent Atoms 175

Software

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