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Crystal structure of sperm whale myoglobin (F46L/H64A mutant) reconstituted with manganese porphycene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1.8 M ammonium sulfate, 100 mM Tris-HCl buffer at pH 8.2, 4% acetone and 10% trehalose
Crystal Properties Matthews coefficient Solvent content 3.14 60.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.673 α = 90 b = 80.174 β = 90 c = 106.595 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 100 PIXEL DECTRIS EIGER X 16M 2020-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.9 50 99.9 0.999 13.8 6.63 39037
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.607
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 44.42 37124 1849 99.86 0.18024 0.17862 0.1894 0.21242 0.2189 RANDOM 46.342
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] -0.98 -1.62 2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.864 r_dihedral_angle_4_deg 22.056 r_dihedral_angle_3_deg 17.619 r_long_range_B_refined 9.993 r_long_range_B_other 9.983 r_scangle_other 8.579 r_scbond_it 5.968 r_dihedral_angle_1_deg 5.706 r_scbond_other 5.686 r_mcangle_it 5.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.864 r_dihedral_angle_4_deg 22.056 r_dihedral_angle_3_deg 17.619 r_long_range_B_refined 9.993 r_long_range_B_other 9.983 r_scangle_other 8.579 r_scbond_it 5.968 r_dihedral_angle_1_deg 5.706 r_scbond_other 5.686 r_mcangle_it 5.421 r_mcangle_other 5.395 r_mcbond_it 4.256 r_mcbond_other 4.224 r_angle_refined_deg 3.945 r_angle_other_deg 1.563 r_chiral_restr 0.1 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_gen_planes_other 0.006 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 2540 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building MOLREP phasing