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T-To-T(High) quaternary transitions in human hemoglobin: betaW37A OXY (10 test sets)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y4F PDB ENTRY 1Y4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10% PEG 6000, 10 MM POTASSIUM
PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE,
10 MG/ML DEOXYHB, PH 7.0, BATCH, TEMPERATURE 298K, 1 ATM N2.
EXPOSING DEOXY CRYSTAL TO LIGAND: A DEOXY CRYSTAL WAS SOAKED
(UNDER 1 ATM NITROGEN) IN SUBSTITUTE MOTHER LIQUOR CONTAINING
13% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM
POTASSIUM CHLORIDE. THE CRYSTAL WAS THEN EXPOSED TO AIR AT 298K
AND DATA WAS COLLECTED AT 298K.
Crystal Properties Matthews coefficient Solvent content 2.56 51.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.89 α = 90 b = 98.92 β = 90 c = 66.83 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 GRAPHITE 1995-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.22 50 97.3 0.076 9.3 7.6 31225
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) 2.22 2.39 87.1 0.222 2.1 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 1Y4F 2.22 10 27710 3063 97.13 0.18466 0.18 0.1833 0.228 0.2286 10 SETS MATCHED TO PDB ENTRY 1Y4F 25.61
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] -0.39 1.03 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.013 r_scangle_it 3.444 r_dihedral_angle_1_deg 3.343 r_scbond_it 2.111 r_angle_refined_deg 1.467 r_mcangle_it 1.423 r_angle_other_deg 1.096 r_mcbond_it 0.734 r_symmetry_vdw_other 0.252 r_nbd_refined 0.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.013 r_scangle_it 3.444 r_dihedral_angle_1_deg 3.343 r_scbond_it 2.111 r_angle_refined_deg 1.467 r_mcangle_it 1.423 r_angle_other_deg 1.096 r_mcbond_it 0.734 r_symmetry_vdw_other 0.252 r_nbd_refined 0.248 r_xyhbond_nbd_refined 0.226 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.209 r_nbd_other 0.205 r_xyhbond_nbd_other 0.148 r_chiral_restr 0.083 r_bond_refined_d 0.026 r_nbtor_other 0.021 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4396 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 180
Software Software Software Name Purpose SDMS data collection SDMS data reduction X-PLOR model building SDMS data scaling X-PLOR phasing REFMAC refinement