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Crystal structure of chlorite dismutase at 3000 eV based on spherical harmonics absorption corrections
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MAU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.15 M MgSO4, 0.1 M MES pH 6.5, 25 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.91 57.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.557 α = 107.21 b = 52.755 β = 99.03 c = 54.952 γ = 109.31
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 12M 2023-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 4.132 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.7 50.35 99.43 0.997 20.22 40.3 13696
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.797 0.99
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 2.7 50.35 13042 688 99.19 0.178 0.17562 0.1812 0.22264 0.2236 RANDOM 29.122
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] 5.02 -0.38 0.25 -1.43 -0.82 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.809 r_dihedral_angle_1_deg 6.586 r_long_range_B_other 6.13 r_long_range_B_refined 6.129 r_scangle_other 4.758 r_dihedral_angle_2_deg 4.13 r_mcangle_other 3.342 r_mcangle_it 3.341 r_scbond_it 2.949 r_scbond_other 2.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.809 r_dihedral_angle_1_deg 6.586 r_long_range_B_other 6.13 r_long_range_B_refined 6.129 r_scangle_other 4.758 r_dihedral_angle_2_deg 4.13 r_mcangle_other 3.342 r_mcangle_it 3.341 r_scbond_it 2.949 r_scbond_other 2.948 r_mcbond_it 2.095 r_mcbond_other 2.094 r_angle_refined_deg 1.468 r_angle_other_deg 0.485 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 3034 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing