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X-ray crystal structure of met F43H/H64A sperm whale myoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ERI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30%(w/v) Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.22 44.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.811 α = 90 b = 49.197 β = 90 c = 77.459 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 77 CCD RIGAKU 2016-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.988 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 30.95 99.3 26.05 3.8 24841
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.3 0.077 0.077 20.1 7.1
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 5ERI 1.5 30.95 23574 1267 99.57 0.14394 0.14306 0.1428 0.15991 0.1595 RANDOM 15.307
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] -0.75 0.27 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.045 r_dihedral_angle_4_deg 12.835 r_dihedral_angle_3_deg 11.665 r_long_range_B_refined 6.95 r_long_range_B_other 6.515 r_scangle_other 5.496 r_dihedral_angle_1_deg 4.798 r_scbond_other 3.678 r_scbond_it 3.674 r_angle_refined_deg 2.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.045 r_dihedral_angle_4_deg 12.835 r_dihedral_angle_3_deg 11.665 r_long_range_B_refined 6.95 r_long_range_B_other 6.515 r_scangle_other 5.496 r_dihedral_angle_1_deg 4.798 r_scbond_other 3.678 r_scbond_it 3.674 r_angle_refined_deg 2.573 r_mcangle_other 2.017 r_mcangle_it 2.016 r_mcbond_it 1.402 r_mcbond_other 1.37 r_angle_other_deg 1.058 r_chiral_restr 0.218 r_bond_refined_d 0.031 r_gen_planes_refined 0.014 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 1203 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling MOLREP phasing HKL-3000 data reduction