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X-ray sequence and high resolution crystal structure of Persian sturgeon methemoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BOM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 0.1 M MES pH 6.5 and 12%(w/v) PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.72 54.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.89 α = 90 b = 62.29 β = 97.67 c = 101.564 γ = 90
Symmetry Space Group I 1 2 1
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 2014-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 1W2B 0.9792 BSRF 1W2B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 52.97 99.98 0.123 7.1 3.7 34936
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.744 100
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 3BOM 1.7 52.97 34936 1802 99.98 0.15957 0.15766 0.1696 0.1956 0.2038 RANDOM 19.137
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.565 r_dihedral_angle_3_deg 13.526 r_dihedral_angle_4_deg 13.483 r_long_range_B_refined 6.111 r_long_range_B_other 6.11 r_dihedral_angle_1_deg 5.972 r_scangle_other 4.282 r_scbond_it 2.929 r_scbond_other 2.929 r_mcangle_other 2.621
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.565 r_dihedral_angle_3_deg 13.526 r_dihedral_angle_4_deg 13.483 r_long_range_B_refined 6.111 r_long_range_B_other 6.11 r_dihedral_angle_1_deg 5.972 r_scangle_other 4.282 r_scbond_it 2.929 r_scbond_other 2.929 r_mcangle_other 2.621 r_mcangle_it 2.618 r_angle_refined_deg 1.999 r_mcbond_it 1.829 r_mcbond_other 1.803 r_angle_other_deg 1.757 r_chiral_restr 0.149 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_gen_planes_other 0.005 r_bond_other_d 0.003 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 2202 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing