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Structural characterization of a bacterial 6PDH reveals aspects of specificity, mechanism and mode of inhibition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PGD PDB ENTRY 2PGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.2 25% PEG 3350, 300MM AMMONIUM ACCETATE, 0.1M SODIUM CACODYLATE, pH 7.20
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.582 α = 90 b = 60.582 β = 90 c = 243.128 γ = 120
Symmetry Space Group P 32 1 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 OSMIC MIRRORS 2004-02-05 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) R Merge I (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 2.4 20 96 0.06 13.7 5.5 19558
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 2.4 2.5 75 0.15 6.7 2.2
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 PDB ENTRY 2PGD 2.4 19.83 18555 1003 96 0.162 0.159 0.1581 0.221 0.2221 RANDOM 27.6
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.893 r_dihedral_angle_4_deg 17.345 r_dihedral_angle_3_deg 16.757 r_dihedral_angle_1_deg 5.213 r_scangle_it 1.978 r_scbond_it 1.204 r_angle_refined_deg 1.155 r_mcangle_it 0.829 r_mcbond_it 0.48 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.893 r_dihedral_angle_4_deg 17.345 r_dihedral_angle_3_deg 16.757 r_dihedral_angle_1_deg 5.213 r_scangle_it 1.978 r_scbond_it 1.204 r_angle_refined_deg 1.155 r_mcangle_it 0.829 r_mcbond_it 0.48 r_nbtor_refined 0.3 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3672 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing