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The Zn-bound dimeric structure of K79H/G80A/H81A myoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VM9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1 M Sodium acetate, 0.1 M Tris-HCl, 25% (w/v) PEG 6,000
Crystal Properties Matthews coefficient Solvent content 1.95 37.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.738 α = 90 b = 63.141 β = 90 c = 79.466 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 PILATUS3 S 6M 2018-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 43.98 100 0.068 0.999 17.7 6.3 18568
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.9 0.732 0.772 2.3 6.6
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 3VM9 2 43.98 17575 946 99.93 0.21575 0.21305 0.2185 0.26504 0.2742 RANDOM 33.233
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] 1.28 -1.07 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.816 r_dihedral_angle_3_deg 15.984 r_dihedral_angle_4_deg 15.391 r_dihedral_angle_1_deg 11.162 r_long_range_B_refined 6.183 r_long_range_B_other 6.158 r_scangle_other 4.846 r_mcangle_it 3.486 r_mcangle_other 3.483 r_scbond_it 3.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.816 r_dihedral_angle_3_deg 15.984 r_dihedral_angle_4_deg 15.391 r_dihedral_angle_1_deg 11.162 r_long_range_B_refined 6.183 r_long_range_B_other 6.158 r_scangle_other 4.846 r_mcangle_it 3.486 r_mcangle_other 3.483 r_scbond_it 3.164 r_scbond_other 3.15 r_mcbond_it 2.369 r_mcbond_other 2.368 r_angle_refined_deg 1.52 r_angle_other_deg 1.317 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 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 2392 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing