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T-To-T(High) quaternary transitions in human hemoglobin: betaW37Y OXY (10 test sets)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y46 PDB ENTRY 1Y46
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 52.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.2 α = 90 b = 99.6 β = 90 c = 67 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 1996-10-02 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 2.75 50 98.9 0.171 5.5 5.3 17171
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) 2.75 2.96 94.9 0.301 1.5 3.9 3230
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 1Y46 2.75 10 14988 1699 98.73 0.20428 0.19647 0.1995 0.27434 0.2681 10 SETS MATCHED TO PDB ENTRY 1Y46 22.25
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] 0.44 0.83 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.338 r_dihedral_angle_1_deg 2.664 r_scangle_it 2.004 r_angle_refined_deg 1.341 r_scbond_it 1.177 r_mcangle_it 0.958 r_mcbond_it 0.497 r_symmetry_hbond_refined 0.304 r_nbd_refined 0.275 r_symmetry_vdw_refined 0.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.338 r_dihedral_angle_1_deg 2.664 r_scangle_it 2.004 r_angle_refined_deg 1.341 r_scbond_it 1.177 r_mcangle_it 0.958 r_mcbond_it 0.497 r_symmetry_hbond_refined 0.304 r_nbd_refined 0.275 r_symmetry_vdw_refined 0.254 r_xyhbond_nbd_refined 0.23 r_chiral_restr 0.083 r_bond_refined_d 0.027 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 4382 Nucleic Acid Atoms Solvent Atoms 134 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