1XZ4
Intersubunit Interactions Associated with Tyr42alpha Stabilize the Quaternary-T Tetramer but are not Major Quaternary Constraints in Deoxyhemoglobin: alphaY42A deoxyhemoglobin no-salt
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1XZ2 | pdb entry 1XZ2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | batch | 4.6 | 298 | 15% PEG 4000, 50 mM sodium acetate, 100 mM ammonium acetate, 3 mM sodium dithionite, 20 mg/ml Hb, pH 4.6, batch, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.1 | α = 90 |
b = 111.9 | β = 90 |
c = 64 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 298 | AREA DETECTOR | SDMS | graphite | 1996-09-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.98 | 50 | 96.7 | 0.065 | 9.8 | 6.5 | 41133 | 41133 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.98 | 2.13 | 84.1 | 0.242 | 1.7 | 2.9 | 7049 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT plus local R-free analysis | pdb entry 1XZ2 | 2 | 10 | 41133 | 36294 | 3999 | 97.98 | 0.18674 | 0.18274 | 0.19 | 0.22372 | 0.22 | 10 mutaully exclusive test sets matched to pdb entry 1XZ2 | 25.021 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
-0.53 | 1.05 | -0.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 16.282 |
r_scangle_it | 4.836 |
r_dihedral_angle_1_deg | 3.853 |
r_scbond_it | 3.022 |
r_angle_refined_deg | 1.89 |
r_mcangle_it | 1.808 |
r_angle_other_deg | 1.187 |
r_mcbond_it | 0.957 |
r_symmetry_vdw_other | 0.41 |
r_symmetry_vdw_refined | 0.358 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4366 |
Nucleic Acid Atoms | |
Solvent Atoms | 182 |
Heterogen Atoms | 172 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SDMS | data reduction |
SDMS | data scaling |
X-PLOR | phasing |