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Low-dose (14.4 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 = 28.471 α = 90 b = 35.084 β = 90 c = 123.111 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 1.03 26.657 99.8 0.154 0.177 0.069 0.997 5.6 6.4 333967
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 1.03 1.111 99.5 3.823 2.643 1.027 0.379 0.7 6.4
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 1.03 33.741 61944 1112 99.67 0.171 0.1703 0.17 0.214 0.2167 11.607
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] 0.265 -1.599 1.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.781 r_dihedral_angle_3_deg 12.966 r_lrange_it 12.318 r_lrange_other 11.018 r_dihedral_angle_2_deg 10.607 r_scangle_it 6.5 r_scangle_other 6.498 r_dihedral_angle_1_deg 4.832 r_scbond_it 4.525 r_scbond_other 4.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.781 r_dihedral_angle_3_deg 12.966 r_lrange_it 12.318 r_lrange_other 11.018 r_dihedral_angle_2_deg 10.607 r_scangle_it 6.5 r_scangle_other 6.498 r_dihedral_angle_1_deg 4.832 r_scbond_it 4.525 r_scbond_other 4.437 r_mcangle_other 4.35 r_mcangle_it 4.334 r_rigid_bond_restr 3.505 r_mcbond_it 3.046 r_mcbond_other 2.912 r_angle_refined_deg 1.897 r_dihedral_angle_other_2_deg 0.868 r_angle_other_deg 0.72 r_symmetry_xyhbond_nbd_refined 0.313 r_xyhbond_nbd_refined 0.272 r_nbd_refined 0.258 r_symmetry_nbd_refined 0.254 r_nbd_other 0.237 r_metal_ion_refined 0.185 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.183 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.074 r_symmetry_metal_ion_refined 0.013 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1188 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing