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T-To-T(High) quaternary transitions in human hemoglobin: betaW37H OXY (2MM IHP, 20% PEG) (10 test sets)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y4B PDB ENTRY 1Y4B
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 2.53 51.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.57 α = 90 b = 98.59 β = 90 c = 66.77 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 2002-11-20 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 2.7 49.39 92.1 0.111 4.3 3.2 16452
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) 2.7 2.92 74.6 0.248 2.7 2.5 2690
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 1Y4B 2.7 10 13741 1551 87.34 0.18813 0.17869 0.182 0.27323 0.2701 10 SETS MATCHED TO PDB ENTRY 1Y4B 33.009
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] 0.99 0.06 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.523 r_scangle_it 4.741 r_dihedral_angle_1_deg 4.403 r_scbond_it 2.884 r_angle_refined_deg 2.477 r_mcangle_it 1.897 r_mcbond_it 0.979 r_nbd_refined 0.319 r_symmetry_vdw_refined 0.31 r_xyhbond_nbd_refined 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.523 r_scangle_it 4.741 r_dihedral_angle_1_deg 4.403 r_scbond_it 2.884 r_angle_refined_deg 2.477 r_mcangle_it 1.897 r_mcbond_it 0.979 r_nbd_refined 0.319 r_symmetry_vdw_refined 0.31 r_xyhbond_nbd_refined 0.217 r_chiral_restr 0.147 r_symmetry_hbond_refined 0.138 r_bond_refined_d 0.027 r_gen_planes_refined 0.008 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 4378 Nucleic Acid Atoms Solvent Atoms 114 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