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Crystal Structure of the sulfite dehydrogenase, SorT R78K mutant from Sinorhizobium meliloti
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M PCB buffer pH 7, 25% PEG1500
Crystal Properties Matthews coefficient Solvent content 2.44 49.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.47 α = 90 b = 95.72 β = 90 c = 109.62 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 CCD ADSC QUANTUM 315r 2013-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.6 72.1 99.8 0.132 0.997 9.6 6.8 102224
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 1.6 1.63 99.6 1.057 1.6 6.6
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 4PW9 1.6 72.1 97033 5110 99.7 0.15644 0.1552 0.1684 0.17962 0.1894 RANDOM 17.477
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] 1.4 -0.51 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.052 r_dihedral_angle_4_deg 14.966 r_dihedral_angle_3_deg 11.297 r_dihedral_angle_1_deg 5.952 r_long_range_B_refined 5.692 r_long_range_B_other 4.936 r_scangle_other 2.657 r_scbond_it 1.656 r_scbond_other 1.656 r_mcangle_other 1.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.052 r_dihedral_angle_4_deg 14.966 r_dihedral_angle_3_deg 11.297 r_dihedral_angle_1_deg 5.952 r_long_range_B_refined 5.692 r_long_range_B_other 4.936 r_scangle_other 2.657 r_scbond_it 1.656 r_scbond_other 1.656 r_mcangle_other 1.579 r_mcangle_it 1.578 r_angle_refined_deg 1.501 r_mcbond_it 0.976 r_mcbond_other 0.973 r_angle_other_deg 0.92 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 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 5147 Nucleic Acid Atoms Solvent Atoms 813 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing