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The dimeric structure of G80A/H81A/H82A 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 0.1M Tris-HCl buffer, 0.1M sodium acetate, 12.5% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.1 41.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.225 α = 90 b = 62.841 β = 90 c = 81.532 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 CCD RAYONIX MX-225 2016-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1
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 1.65 50 99.9 0.092 23.3 6.5 34523
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 1.65 1.68 0.784
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 1.65 49.77 32712 1756 99.47 0.19363 0.19174 0.2021 0.2305 0.2382 RANDOM 19.351
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] 0.24 -0.1 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.276 r_dihedral_angle_3_deg 14.995 r_dihedral_angle_4_deg 5.012 r_dihedral_angle_1_deg 4.846 r_long_range_B_refined 3.913 r_long_range_B_other 3.901 r_scangle_other 2.925 r_angle_refined_deg 1.933 r_scbond_it 1.862 r_scbond_other 1.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.276 r_dihedral_angle_3_deg 14.995 r_dihedral_angle_4_deg 5.012 r_dihedral_angle_1_deg 4.846 r_long_range_B_refined 3.913 r_long_range_B_other 3.901 r_scangle_other 2.925 r_angle_refined_deg 1.933 r_scbond_it 1.862 r_scbond_other 1.857 r_mcangle_it 1.479 r_mcangle_other 1.479 r_mcbond_it 1.019 r_mcbond_other 1.019 r_angle_other_deg 0.916 r_chiral_restr 0.143 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.007 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 2380 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing