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X-ray crystal structure of met F43H/H64A sperm whale myoglobin in complex with nitric oxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30%(w/v) Polyethylene glycol 8,000, 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.24 44.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.69 α = 90 b = 49.528 β = 90 c = 77.598 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD RIGAKU 2016-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.988 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 50 99.8 0.073 0.073 14.6 3.4 23916
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.8 0.073 0.073 21 6.4
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 4OF9 1.5 41.75 23916 1284 99.84 0.14191 0.14097 0.1397 0.1594 0.1591 RANDOM 11.296
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] -0.32 0.01 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.457 r_dihedral_angle_4_deg 17.732 r_dihedral_angle_3_deg 11.3 r_long_range_B_refined 6.551 r_long_range_B_other 5.641 r_dihedral_angle_1_deg 4.696 r_scangle_other 4.329 r_scbond_other 2.869 r_scbond_it 2.867 r_angle_refined_deg 2.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.457 r_dihedral_angle_4_deg 17.732 r_dihedral_angle_3_deg 11.3 r_long_range_B_refined 6.551 r_long_range_B_other 5.641 r_dihedral_angle_1_deg 4.696 r_scangle_other 4.329 r_scbond_other 2.869 r_scbond_it 2.867 r_angle_refined_deg 2.356 r_mcangle_other 1.418 r_mcangle_it 1.402 r_mcbond_it 1.018 r_angle_other_deg 0.974 r_mcbond_other 0.953 r_chiral_restr 0.162 r_bond_refined_d 0.027 r_gen_planes_refined 0.015 r_gen_planes_other 0.008 r_bond_other_d 0.001 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 1203 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling MOLREP phasing HKL-3000 data reduction