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A sperm whale myoglobin double mutant L29H/F43Y Mb with a Tyr-heme cross-link
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QAU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.2 M Sodium acetate trihydrate,0.1 M Sodium cacodylate trihydrate pH 6.5,30% w/v Polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.2 44.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.062 α = 90 b = 48.348 β = 90 c = 79.141 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 MAR CCD 165 mm 2015-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.988 SSRF BL17U
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 1.793 50 99.7 19.8 13 14678
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.793 1.83 100 0.524 12.9 12.9
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 4QAU 1.793 41.26 13889 745 97.57 0.15796 0.15677 0.1685 0.18083 0.1956 RANDOM 22.367
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] -1.17 0.18 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.535 r_dihedral_angle_4_deg 29.185 r_dihedral_angle_3_deg 11.65 r_long_range_B_refined 7.937 r_long_range_B_other 7.707 r_scangle_other 6.351 r_dihedral_angle_1_deg 5.047 r_scbond_other 4.208 r_scbond_it 4.204 r_mcangle_other 2.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.535 r_dihedral_angle_4_deg 29.185 r_dihedral_angle_3_deg 11.65 r_long_range_B_refined 7.937 r_long_range_B_other 7.707 r_scangle_other 6.351 r_dihedral_angle_1_deg 5.047 r_scbond_other 4.208 r_scbond_it 4.204 r_mcangle_other 2.843 r_mcangle_it 2.84 r_angle_refined_deg 2.228 r_mcbond_it 2.095 r_mcbond_other 2.026 r_angle_other_deg 1.482 r_chiral_restr 0.185 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_gen_planes_other 0.007 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 1213 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DENZO data reduction HKL-2000 data scaling PHASER phasing