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Higher-dose (676.8 kGy) structure of horse-heart myoglobin at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WLA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 3.5 M ammonium sulphate, 0.1 M Tris-HCl pH 7.4
Crystal Properties Matthews coefficient Solvent content 1.82 32.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.484 α = 90 b = 35.101 β = 90 c = 123.16 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 6M 2024-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.9795 ESRF BM07
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.103 27.743 99.9 0.161 0.194 0.076 0.995 4.9 6.4 50652
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.103 1.122 99.8 3.848 3.072 1.209 0.334 0.6 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.1 33.757 51125 999 99.754 0.164 0.1632 0.1707 0.2008 0.2064 11.88
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] 0.037 0.019 -0.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.25 r_dihedral_angle_3_deg 13.418 r_dihedral_angle_2_deg 12.983 r_lrange_it 10.497 r_lrange_other 9.847 r_scangle_it 7.079 r_scangle_other 7.076 r_dihedral_angle_1_deg 4.937 r_scbond_it 4.904 r_scbond_other 4.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.25 r_dihedral_angle_3_deg 13.418 r_dihedral_angle_2_deg 12.983 r_lrange_it 10.497 r_lrange_other 9.847 r_scangle_it 7.079 r_scangle_other 7.076 r_dihedral_angle_1_deg 4.937 r_scbond_it 4.904 r_scbond_other 4.827 r_mcangle_other 4.133 r_mcangle_it 4.119 r_rigid_bond_restr 3.66 r_mcbond_it 2.975 r_mcbond_other 2.904 r_angle_refined_deg 1.934 r_dihedral_angle_other_2_deg 1.52 r_angle_other_deg 0.732 r_symmetry_xyhbond_nbd_refined 0.319 r_xyhbond_nbd_refined 0.252 r_symmetry_nbd_refined 0.24 r_nbd_refined 0.234 r_nbd_other 0.227 r_nbtor_refined 0.184 r_symmetry_nbd_other 0.182 r_metal_ion_refined 0.153 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.072 r_symmetry_metal_ion_refined 0.072 r_symmetry_xyhbond_nbd_other 0.053 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1182 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing