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X-ray crystal structure of F46C myoglobin with a covalently linked phenol group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EHX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.2 43.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.719 α = 90 b = 48.172 β = 90 c = 78.906 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 EIGER2 S 9M 2022-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9791 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.46 50 99.8 0.106 0.047 0.996 16 6.1 27141 4.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.54 0.46 0.248 0.878 3.2
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 (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 1.46 41.12 25749 1335 99.69 0.15236 0.14985 0.1542 0.20039 0.1967 RANDOM 9.904
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] 0.1 -0.23 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.563 r_dihedral_angle_4_deg 16.596 r_dihedral_angle_3_deg 12.51 r_dihedral_angle_1_deg 4.908 r_scbond_it 2.452 r_mcangle_it 2.244 r_angle_refined_deg 2.213 r_mcbond_it 1.721 r_chiral_restr 0.116 r_bond_refined_d 0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.563 r_dihedral_angle_4_deg 16.596 r_dihedral_angle_3_deg 12.51 r_dihedral_angle_1_deg 4.908 r_scbond_it 2.452 r_mcangle_it 2.244 r_angle_refined_deg 2.213 r_mcbond_it 1.721 r_chiral_restr 0.116 r_bond_refined_d 0.022 r_gen_planes_refined 0.016 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1211 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing