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Crystal structure of Steptococcus suis mannonate dehydratase with metal Mn++
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TZ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.2M potassium/sodium tartrate, 0.1M sodium citrate, 1M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.59 52.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.69 α = 90 b = 105.69 β = 90 c = 159.572 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2007-12-10 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 2.8 50 94 5 25673
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 95
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1tz9 2.9 44.06 3 19634 1064 99.77 0.28 0.2368 0.23401 0.28585 0.2651 RANDOM 41.716
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] -1.1 -1.1 2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.973 r_dihedral_angle_4_deg 20.23 r_dihedral_angle_3_deg 19.869 r_dihedral_angle_1_deg 7.293 r_scangle_it 2.2 r_angle_refined_deg 1.636 r_scbond_it 1.341 r_mcangle_it 1.206 r_mcbond_it 0.675 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.973 r_dihedral_angle_4_deg 20.23 r_dihedral_angle_3_deg 19.869 r_dihedral_angle_1_deg 7.293 r_scangle_it 2.2 r_angle_refined_deg 1.636 r_scbond_it 1.341 r_mcangle_it 1.206 r_mcbond_it 0.675 r_nbtor_refined 0.322 r_symmetry_hbond_refined 0.289 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.238 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5471 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose CrystalClear data collection MOSFLM data reduction REFMAC refinement SCALA data scaling