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T-To-T(High) quaternary transitions in human hemoglobin: betaW37E OXY (10 test sets)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y4P PDB ENTRY 1Y4P
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 2.58 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.07 α = 90 b = 99.28 β = 90 c = 67.02 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 1998-09-27 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 2.11 50 97.6 0.083 9.2 6.9 36695
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) 2.11 2.27 88.5 0.273 1.6 3.3 6536
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 1Y4P 2.11 10 32553 3624 97.23 0.19871 0.19394 0.1961 0.24193 0.2399 10 SETS MATCHED TO PDB ENTRY 1Y4P 27.925
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] -0.98 1.58 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.22 r_scangle_it 4.152 r_dihedral_angle_1_deg 3.832 r_scbond_it 2.63 r_angle_refined_deg 1.707 r_mcangle_it 1.657 r_angle_other_deg 1.195 r_mcbond_it 0.887 r_nbd_refined 0.258 r_symmetry_hbond_refined 0.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.22 r_scangle_it 4.152 r_dihedral_angle_1_deg 3.832 r_scbond_it 2.63 r_angle_refined_deg 1.707 r_mcangle_it 1.657 r_angle_other_deg 1.195 r_mcbond_it 0.887 r_nbd_refined 0.258 r_symmetry_hbond_refined 0.242 r_symmetry_vdw_other 0.229 r_xyhbond_nbd_refined 0.215 r_nbd_other 0.212 r_xyhbond_nbd_other 0.204 r_symmetry_vdw_refined 0.129 r_chiral_restr 0.099 r_bond_refined_d 0.03 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other 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 4331 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 180
Software Software Software Name Purpose SDMS data collection SDMS data reduction X-PLOR model building REFMAC refinement SDMS data scaling X-PLOR phasing