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T-to-T(High) quaternary transitions in human hemoglobin: HbA OXY (2MM 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 2.2 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 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.1 α = 90 b = 99.6 β = 90 c = 66.1 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 2000-12-14 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 2.2 34.77 93.7 0.073 4.7 3.1 31525
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) 2.2 2.37 87.7 0.266 3.3 2.7 8798
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 2.2 10 26043 2971 88.36 0.19424 0.18956 0.1987 0.23589 0.2386 10 SETS MATCHED TO PDB ENTRY 1RQ3 30.531
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] -0.41 1.4 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.998 r_dihedral_angle_1_deg 3.099 r_scangle_it 2.303 r_scbond_it 1.401 r_angle_refined_deg 1.255 r_angle_other_deg 1.06 r_mcangle_it 0.99 r_mcbond_it 0.52 r_nbd_refined 0.239 r_nbd_other 0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.998 r_dihedral_angle_1_deg 3.099 r_scangle_it 2.303 r_scbond_it 1.401 r_angle_refined_deg 1.255 r_angle_other_deg 1.06 r_mcangle_it 0.99 r_mcbond_it 0.52 r_nbd_refined 0.239 r_nbd_other 0.197 r_symmetry_vdw_other 0.189 r_xyhbond_nbd_refined 0.183 r_symmetry_hbond_refined 0.173 r_symmetry_vdw_refined 0.113 r_chiral_restr 0.074 r_xyhbond_nbd_other 0.054 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 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 143 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