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Quaternary complex structure of gluconate 5-dehydrogenase from streptococcus suis type 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CXR
Crystallization Crystal Properties Matthews coefficient Solvent content 2.13 42.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.244 α = 90 b = 75.272 β = 90 c = 98.7 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 59.87 24607
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 25.87 0.068 0.15
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 3CXR 1.9 25.87 20183 1072 99.8 0.194 0.191 0.1899 0.242 0.2426 RANDOM 24.2
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] -1.67 1.08 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.8 r_dihedral_angle_4_deg 15.198 r_dihedral_angle_3_deg 13.732 r_dihedral_angle_1_deg 6.241 r_scangle_it 3.465 r_scbond_it 2.391 r_angle_refined_deg 1.637 r_mcangle_it 1.317 r_mcbond_it 0.918 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.8 r_dihedral_angle_4_deg 15.198 r_dihedral_angle_3_deg 13.732 r_dihedral_angle_1_deg 6.241 r_scangle_it 3.465 r_scbond_it 2.391 r_angle_refined_deg 1.637 r_mcangle_it 1.317 r_mcbond_it 0.918 r_nbtor_refined 0.297 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.202 r_symmetry_hbond_refined 0.188 r_chiral_restr 0.16 r_xyhbond_nbd_refined 0.155 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1884 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 62
Software Software Software Name Purpose AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling