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Crystal structure of KGPDC from Streptococcus mutans in complex with D-R5P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EXT PDB ENTRY 3EXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 0.2M KCl, 0.05M HEPES, pH7.5, 35%(v/v) pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.51 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.152 α = 90 b = 124.249 β = 90 c = 130.066 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 BRUKER SMART 6000 2008-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 19.74 93.41 0.077 31798
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 3EXT 2.5 19.74 29234 1548 90.91 0.18661 0.18357 0.1821 0.24386 0.2421 RANDOM 22.278
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] -0.28 -0.34 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.35 r_dihedral_angle_4_deg 24.645 r_dihedral_angle_3_deg 17.396 r_dihedral_angle_1_deg 6.789 r_scangle_it 3.014 r_scbond_it 1.901 r_angle_refined_deg 1.367 r_mcangle_it 1.24 r_mcbond_it 0.813 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.35 r_dihedral_angle_4_deg 24.645 r_dihedral_angle_3_deg 17.396 r_dihedral_angle_1_deg 6.789 r_scangle_it 3.014 r_scbond_it 1.901 r_angle_refined_deg 1.367 r_mcangle_it 1.24 r_mcbond_it 0.813 r_nbtor_refined 0.308 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.14 r_symmetry_vdw_refined 0.123 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 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 6339 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 27
Software Software Software Name Purpose SAINT data scaling REFMAC refinement PDB_EXTRACT data extraction