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T-To-T(High) quaternary transitions in human hemoglobin: betaW37G OXY (10 test sets)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y4G PDB ENTRY 1Y4G
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 52.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.25 α = 90 b = 99.22 β = 90 c = 66.89 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 1997-06-21 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 2.12 50 96.7 0.082 9.6 6.7 35935
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) 2.12 2.28 86.1 0.296 1.1 3 6288
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 1Y4G 2.12 10 31757 3529 96.25 0.20599 0.20069 0.2036 0.25415 0.2517 10 SETS MATCHED TO PDB ENTRY 1Y4G 30.324
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] -0.56 0.96 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.933 r_scangle_it 4.27 r_dihedral_angle_1_deg 3.902 r_scbond_it 2.68 r_angle_refined_deg 1.783 r_mcangle_it 1.726 r_angle_other_deg 1.228 r_mcbond_it 0.927 r_nbd_refined 0.256 r_xyhbond_nbd_other 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.933 r_scangle_it 4.27 r_dihedral_angle_1_deg 3.902 r_scbond_it 2.68 r_angle_refined_deg 1.783 r_mcangle_it 1.726 r_angle_other_deg 1.228 r_mcbond_it 0.927 r_nbd_refined 0.256 r_xyhbond_nbd_other 0.247 r_xyhbond_nbd_refined 0.233 r_nbd_other 0.213 r_symmetry_hbond_refined 0.204 r_symmetry_vdw_other 0.202 r_symmetry_vdw_refined 0.181 r_chiral_restr 0.109 r_bond_refined_d 0.033 r_nbtor_other 0.012 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_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 4387 Nucleic Acid Atoms Solvent Atoms 112 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