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human (alpha met/beta hemichrome) hemoglobin with S-nitrosation at beta-Cys93
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 298 sodium phosphate, potassium phosphate, toluene
Crystal Properties Matthews coefficient Solvent content 2.21 44.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.287 α = 90 b = 53.287 β = 90 c = 193.464 γ = 90
Symmetry Space Group P 41 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 100 PIXEL DECTRIS PILATUS3 S 6M 2015-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.987 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 51.37 99.9 40 16.9 23560
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 8
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 3P5Q 1.85 51.37 23560 1206 99.91 0.22778 0.22491 0.2323 0.28222 0.2858 RANDOM 22.978
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] 0.07 0.07 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.098 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_4_deg 14.108 r_dihedral_angle_1_deg 5.786 r_long_range_B_refined 5.283 r_long_range_B_other 5.228 r_scangle_other 3.555 r_mcangle_it 2.826 r_mcangle_other 2.825 r_scbond_it 2.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.098 r_dihedral_angle_3_deg 14.879 r_dihedral_angle_4_deg 14.108 r_dihedral_angle_1_deg 5.786 r_long_range_B_refined 5.283 r_long_range_B_other 5.228 r_scangle_other 3.555 r_mcangle_it 2.826 r_mcangle_other 2.825 r_scbond_it 2.281 r_scbond_other 2.281 r_mcbond_it 1.931 r_mcbond_other 1.93 r_angle_refined_deg 1.9 r_angle_other_deg 1.087 r_chiral_restr 0.129 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2172 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing