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T-to-thigh quaternary transitions in human hemoglobin: betaW37A oxy (2.2MM IHP, 13% PEG) (1 test set)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y0T PDB ENTRY 1Y0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 298 10% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, 1 ATM N2, pH 7.00, batch, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.57 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.2 α = 90 b = 99 β = 90 c = 66.8 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 AREA DETECTOR SDMS 1996-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall 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 2.4 50 97.1 0.107 7.2 4.9 24954
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) 2.4 2.58 90.4 0.281 1.6 3.6 4549
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 PDB ENTRY 1Y0T 2.4 10 2 24197 22833 2076 97.1 0.185 0.1828 0.273 0.1831 MATCHED TO PDB ENTRY 1Y0T 27.18
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 33.5 p_staggered_tor 21.8 p_scangle_it 8.418 p_scbond_it 6.248 p_mcangle_it 3.754 p_mcbond_it 2.518 p_planar_tor 2.4 p_multtor_nbd 0.184 p_xyhbond_nbd 0.184 p_singtor_nbd 0.174
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 33.5 p_staggered_tor 21.8 p_scangle_it 8.418 p_scbond_it 6.248 p_mcangle_it 3.754 p_mcbond_it 2.518 p_planar_tor 2.4 p_multtor_nbd 0.184 p_xyhbond_nbd 0.184 p_singtor_nbd 0.174 p_hb_or_metal_coord 0.132 p_chiral_restr 0.13 p_angle_d 0.025 p_planar_d 0.025 p_bond_d 0.01 p_plane_restr 0.009 p_angle_deg p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4368 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 180
Software Software Software Name Purpose SDMS data collection SDMS data reduction X-PLOR model building PROLSQ refinement SDMS data scaling X-PLOR phasing