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X-ray crystal structure of met I107Y sperm whale myoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QAU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30%(w/v) Polyethylene glycol 8,000, 0.1M Sodium cacodylate trihydrate pH 6.5, 0.2M Sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.911 α = 90 b = 48.56 β = 90 c = 78.184 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 PIXEL DECTRIS PILATUS3 6M 2016-01-01 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) 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 1.6 50 96.2 0.079 34.4 6.4 19658
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 1.6 1.63 94.8 6.8
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 4QAU 1.61 35.57 18623 1002 96.12 0.16743 0.16594 0.1758 0.19418 0.1986 RANDOM 26.091
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] -1.85 0.35 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.398 r_dihedral_angle_4_deg 20.069 r_dihedral_angle_3_deg 13.121 r_long_range_B_refined 6.631 r_long_range_B_other 6.328 r_scangle_other 5.256 r_dihedral_angle_1_deg 4.699 r_scbond_other 3.632 r_scbond_it 3.629 r_mcangle_it 2.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.398 r_dihedral_angle_4_deg 20.069 r_dihedral_angle_3_deg 13.121 r_long_range_B_refined 6.631 r_long_range_B_other 6.328 r_scangle_other 5.256 r_dihedral_angle_1_deg 4.699 r_scbond_other 3.632 r_scbond_it 3.629 r_mcangle_it 2.565 r_mcangle_other 2.564 r_angle_refined_deg 2.105 r_mcbond_it 1.883 r_mcbond_other 1.849 r_angle_other_deg 0.925 r_chiral_restr 0.157 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 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 1220 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction PHENIX model building MOLREP phasing HKL-3000 data scaling