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X-ray structure of F43Y/H64D sperm whale myoglobin in complex with TCP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30% PEG8000, 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.899 α = 90 b = 49.477 β = 90 c = 77.333 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 2018-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) 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 1.8 50 99.7 0.107 0.088 0.047 24.5 6.3 14844
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 98.2 0.694 0.78 0.294 1.48 5.4
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 2EB8 1.8 35.46 14051 749 99.57 0.18679 0.18457 0.196 0.22897 0.2379 RANDOM 31.197
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] -0.09 0.04 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.62 r_dihedral_angle_4_deg 23.038 r_dihedral_angle_3_deg 16.455 r_long_range_B_refined 8.944 r_long_range_B_other 8.902 r_dihedral_angle_1_deg 6.338 r_scangle_other 5.64 r_mcangle_it 3.967 r_mcangle_other 3.957 r_scbond_it 3.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.62 r_dihedral_angle_4_deg 23.038 r_dihedral_angle_3_deg 16.455 r_long_range_B_refined 8.944 r_long_range_B_other 8.902 r_dihedral_angle_1_deg 6.338 r_scangle_other 5.64 r_mcangle_it 3.967 r_mcangle_other 3.957 r_scbond_it 3.732 r_scbond_other 3.701 r_angle_refined_deg 3.123 r_mcbond_it 2.744 r_mcbond_other 2.733 r_angle_other_deg 0.99 r_chiral_restr 0.162 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 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 1215 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing