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Crystallographic Analysis of the Interaction of Nitric Oxide with Quaternary-T Human Hemoglobin. Hemoglobin exposed to NO under anerobic conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RQ3 pdb id 1RQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 298 10 mg/mL
human hemoglobin, 10 mM potassium phosphate, 100 mM potassium chloride, 10-12% PEG 6000, 3
mM sodium dithionite (under anaerobic conditions), BATCH METHOD, temperature 298K, pH 7
Crystal Properties Matthews coefficient Solvent content 2.56 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97 α = 90 b = 99.3 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 298 AREA DETECTOR SDMS 1998-06-20 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 2.11 39.841 96.9 0.094 8.1 6.3 37996 37996
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) 2.11 2.27 87.1 0.272 1.5 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 id 1RQ3 2.11 10 30288 30288 3440 89.73 0.18648 0.18136 0.1857 0.23217 0.2365 matched to that in PDB id 1RQ3 25.816
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] -1.08 1.31 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.769 r_scangle_it 3.831 r_dihedral_angle_1_deg 3.651 r_scbond_it 2.34 r_angle_refined_deg 1.628 r_mcangle_it 1.526 r_mcbond_it 0.801 r_angle_other_deg 0.793 r_nbd_refined 0.247 r_xyhbond_nbd_refined 0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.769 r_scangle_it 3.831 r_dihedral_angle_1_deg 3.651 r_scbond_it 2.34 r_angle_refined_deg 1.628 r_mcangle_it 1.526 r_mcbond_it 0.801 r_angle_other_deg 0.793 r_nbd_refined 0.247 r_xyhbond_nbd_refined 0.206 r_nbd_other 0.194 r_symmetry_vdw_other 0.175 r_symmetry_hbond_refined 0.122 r_xyhbond_nbd_other 0.111 r_chiral_restr 0.094 r_symmetry_vdw_refined 0.055 r_bond_refined_d 0.022 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 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_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 176 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement SDMS data reduction SDMS data scaling X-PLOR phasing