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The Ni-bound dimeric structure of K78H/G80A/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 0.1 M Sodium acetate, 0.1 M Tris-HCl, 25% (w/v) PEG 6,000
Crystal Properties Matthews coefficient Solvent content 2.21 44.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.819 α = 90 b = 63.276 β = 90 c = 83.267 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 2018-10-26 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 1.91 46.98 100 0.073 0.999 13.9 6.4 23917
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 1.91 2.02 0.919 0.705 1.8 6.5
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 1.91 46.93 22676 1191 99.96 0.21153 0.20889 0.2155 0.26226 0.2695 RANDOM 37.486
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] 2.01 -1.13 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.65 r_dihedral_angle_3_deg 14.913 r_long_range_B_refined 6.811 r_long_range_B_other 6.791 r_dihedral_angle_4_deg 6.605 r_scangle_other 5.436 r_dihedral_angle_1_deg 5.382 r_mcangle_it 3.766 r_mcangle_other 3.752 r_scbond_it 3.554
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.65 r_dihedral_angle_3_deg 14.913 r_long_range_B_refined 6.811 r_long_range_B_other 6.791 r_dihedral_angle_4_deg 6.605 r_scangle_other 5.436 r_dihedral_angle_1_deg 5.382 r_mcangle_it 3.766 r_mcangle_other 3.752 r_scbond_it 3.554 r_scbond_other 3.54 r_mcbond_it 2.816 r_mcbond_other 2.785 r_angle_refined_deg 1.52 r_angle_other_deg 1.357 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 133 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing