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Crystal structure of Chlorite Dismutase from Magnetospirillum sp. in complex with thiocyanate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q08 PDB ENTRY 3Q08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 20% PEG 4000, 0.1 M TRIS-HCL PH 8.5, 0.2 M LI2SO4
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.026 α = 90 b = 124.482 β = 92.91 c = 133.376 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 PIXEL DECTRIS PILATUS 2014-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.75 49.11 99.7 0.08 12 4.6 261153 2.2
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 1.75 1.78 99.8 0.6 2.2 4.7
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 PDB ENTRY 3Q08 1.75 49.11 248487 12628 99.66 0.15287 0.15129 0.164 0.18349 0.1923 RANDOM 18.924
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] 0.23 0.06 0.69 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.508 r_dihedral_angle_4_deg 18.13 r_dihedral_angle_3_deg 13.039 r_dihedral_angle_1_deg 6.357 r_scbond_it 6.114 r_mcangle_it 4.325 r_mcbond_it 3.971 r_mcbond_other 3.971 r_angle_refined_deg 1.781 r_angle_other_deg 0.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.508 r_dihedral_angle_4_deg 18.13 r_dihedral_angle_3_deg 13.039 r_dihedral_angle_1_deg 6.357 r_scbond_it 6.114 r_mcangle_it 4.325 r_mcbond_it 3.971 r_mcbond_other 3.971 r_angle_refined_deg 1.781 r_angle_other_deg 0.882 r_chiral_restr 0.12 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_gen_planes_other 0.007 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18900 Nucleic Acid Atoms Solvent Atoms 2083 Heterogen Atoms 544
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing