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X-ray structure of F43Y/H64D sperm whale myoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30% w/v Polyethylene glycol 8000, 0.1 M Sodium cacodylate trihydrate pH 6.5, 0.2 M Sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 2.21 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.841 α = 90 b = 49.327 β = 90 c = 77.531 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 PILATUS 2M 2018-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) 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 99 0.075 0.056 0.032 16.1 6.4 20810
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 0.424 0.39 0.183 3 6.3
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 2JHO 1.6 31.01 19690 1068 99.8 0.16865 0.16648 0.183 0.20989 0.2194 RANDOM 15.911
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] -0.14 0.04 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.181 r_dihedral_angle_4_deg 23.289 r_dihedral_angle_3_deg 13.153 r_dihedral_angle_1_deg 7.147 r_long_range_B_refined 6.246 r_long_range_B_other 5.92 r_scangle_other 3.98 r_angle_refined_deg 3.605 r_scbond_other 2.635 r_scbond_it 2.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.181 r_dihedral_angle_4_deg 23.289 r_dihedral_angle_3_deg 13.153 r_dihedral_angle_1_deg 7.147 r_long_range_B_refined 6.246 r_long_range_B_other 5.92 r_scangle_other 3.98 r_angle_refined_deg 3.605 r_scbond_other 2.635 r_scbond_it 2.633 r_mcangle_it 2.332 r_mcangle_other 2.332 r_mcbond_it 1.565 r_mcbond_other 1.561 r_angle_other_deg 1.151 r_chiral_restr 0.219 r_bond_refined_d 0.024 r_gen_planes_refined 0.014 r_gen_planes_other 0.006 r_bond_other_d 0.002 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 1215 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing