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X-ray sequence and high resolution crystal structure of Starry 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 7.5 292 0.1M Hepes sodium pH 7.5, 20%(w/v) PEG4000 and 10%(v/v) 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.58 52.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.98 α = 90 b = 61.41 β = 97.75 c = 102.366 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 2.2 52.53 99.08 0.063 15.8 3.8 16020
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 98.9 0.096 11.8 3.8
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 2.2 52.53 16020 800 99.08 0.14046 0.13758 0.1509 0.19495 0.2056 RANDOM 18.54
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.78 r_dihedral_angle_3_deg 14.369 r_dihedral_angle_4_deg 11.998 r_dihedral_angle_1_deg 6.049 r_long_range_B_refined 5.684 r_long_range_B_other 5.681 r_scangle_other 3.675 r_mcangle_it 2.536 r_mcangle_other 2.536 r_scbond_it 2.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.78 r_dihedral_angle_3_deg 14.369 r_dihedral_angle_4_deg 11.998 r_dihedral_angle_1_deg 6.049 r_long_range_B_refined 5.684 r_long_range_B_other 5.681 r_scangle_other 3.675 r_mcangle_it 2.536 r_mcangle_other 2.536 r_scbond_it 2.367 r_scbond_other 2.363 r_angle_refined_deg 1.863 r_mcbond_it 1.606 r_mcbond_other 1.603 r_angle_other_deg 1.349 r_chiral_restr 0.138 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 2205 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing