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Crystal structure of gluconate 5-dehydrogase from streptococcus suis type 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VL8
Crystallization Crystal Properties Matthews coefficient Solvent content 2.11 41.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.147 α = 90 b = 75.378 β = 90 c = 97.674 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 1.5418
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 1.9 59.66 19757
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 30.56 4.2 19757
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 (All) 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 1vl8 2 30.56 16716 888 97.06 0.21 0.19193 0.19111 0.1869 0.20772 0.2016 RANDOM 22.88
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] -1.2 0.33 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.824 r_dihedral_angle_4_deg 15.257 r_dihedral_angle_3_deg 14.238 r_dihedral_angle_1_deg 5.533 r_scangle_it 3.026 r_scbond_it 2.077 r_angle_refined_deg 1.243 r_mcangle_it 1.182 r_mcbond_it 0.724 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.824 r_dihedral_angle_4_deg 15.257 r_dihedral_angle_3_deg 14.238 r_dihedral_angle_1_deg 5.533 r_scangle_it 3.026 r_scbond_it 2.077 r_angle_refined_deg 1.243 r_mcangle_it 1.182 r_mcbond_it 0.724 r_nbtor_refined 0.304 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.103 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1938 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling AMoRE phasing