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Structure of a putative pyruvate dehydrogenase from the photosynthetic bacterium Rhodopseudomonas palustrus CGA009
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 278 0.1M phosphate critrate pH 4.2
1.6M NaH2PO4, 0.4M K2HPO4, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.67 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.7 α = 90 b = 64.995 β = 90 c = 116.89 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 ADSC QUANTUM 315r 2009-04-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97948, 0.97935 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 1.8 50 99.6 0.09 8.4 8 46379 46379 -3
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 1.8 1.83 100 0.596 6.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.8 43.48 46230 43887 2343 99.58 0.16839 0.16692 0.182 0.19545 0.2053 RANDOM 12.894
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] 0.06 0.45 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.896 r_dihedral_angle_3_deg 14.038 r_dihedral_angle_4_deg 12.502 r_dihedral_angle_1_deg 5.158 r_scangle_it 4.49 r_scbond_it 2.735 r_mcangle_it 1.556 r_angle_refined_deg 1.407 r_angle_other_deg 0.885 r_mcbond_it 0.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.896 r_dihedral_angle_3_deg 14.038 r_dihedral_angle_4_deg 12.502 r_dihedral_angle_1_deg 5.158 r_scangle_it 4.49 r_scbond_it 2.735 r_mcangle_it 1.556 r_angle_refined_deg 1.407 r_angle_other_deg 0.885 r_mcbond_it 0.801 r_mcbond_other 0.213 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2948 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 45
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building