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T-To-T(High) quaternary transitions in human hemoglobin: HbA OXY (5.0MM IHP, 20% PEG) (10 test sets)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RQ3 PDB ENTRY 1RQ3
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 20% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM POTASSIUM CHLORIDE, AND 5.0 MM IHP. THE IHP-STABILIZED CRYSTAL WAS THEN EXPOSED TO 1 ATM OF OXYGEN AT 177K AND DATA WAS COLLECTED AT 169K.
Crystal Properties Matthews coefficient Solvent content 2.56 51.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.92 α = 90 b = 99.19 β = 90 c = 66.06 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 169 IMAGE PLATE RIGAKU RAXIS IV OSMIC MIRRORS 2001-11-26 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 2.1 34.71 97.1 0.055 10.6 3.7 32696
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) 2.1 2.27 61.2 0.136 5 3.1 4049
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 1RQ3 2.1 10 28556 3229 84.81 0.1715 0.16734 0.1796 0.20838 0.2193 10 SETS MATCHED TO PDB ENTRY 1RQ3 23.835
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] -0.66 0.68 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.061 r_scangle_it 3.954 r_dihedral_angle_1_deg 3.671 r_scbond_it 2.511 r_mcangle_it 1.574 r_angle_refined_deg 1.493 r_angle_other_deg 1.132 r_mcbond_it 0.829 r_symmetry_vdw_other 0.3 r_nbd_refined 0.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.061 r_scangle_it 3.954 r_dihedral_angle_1_deg 3.671 r_scbond_it 2.511 r_mcangle_it 1.574 r_angle_refined_deg 1.493 r_angle_other_deg 1.132 r_mcbond_it 0.829 r_symmetry_vdw_other 0.3 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.213 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.096 r_xyhbond_nbd_other 0.081 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 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 4384 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 180
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling X-PLOR model building REFMAC refinement CCP4 data scaling X-PLOR phasing