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Crystal structure of 2-dehydropantoate 2-reductase from Porphyromonas gingivalis W83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.2M Ammonium sulfate, 0.1M MES, 30% PEG MME5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.18 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.577 α = 90 b = 79.577 β = 90 c = 98.26 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 315 Mirror 2007-03-02 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97925, 0.97938 APS 19-ID
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 2.15 62 95.3 0.132 14.5 6.2 16966 16966 24.83
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 2.15 2.2 67.4 0.475 1.8 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.15 41.81 16055 16055 866 95.33 0.19839 0.19493 0.26479 0.2787 RANDOM 21.634
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] -0.94 -0.94 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.654 r_dihedral_angle_3_deg 19.52 r_dihedral_angle_4_deg 19.216 r_dihedral_angle_1_deg 6.688 r_scangle_it 3.288 r_scbond_it 2.196 r_angle_refined_deg 1.748 r_mcangle_it 1.486 r_mcbond_it 0.966 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.654 r_dihedral_angle_3_deg 19.52 r_dihedral_angle_4_deg 19.216 r_dihedral_angle_1_deg 6.688 r_scangle_it 3.288 r_scbond_it 2.196 r_angle_refined_deg 1.748 r_mcangle_it 1.486 r_mcbond_it 0.966 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.165 r_chiral_restr 0.117 r_bond_refined_d 0.017 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 2241 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MLPHARE phasing HKL-3000 phasing