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Crystal structure of pyruvate oxidoreductase subunit PORC (EC 1.2.7.1) (TM0015) from Thermotoga maritima at 2.12 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 NANODROP, 0.8M Ammonium sulfate, 0.1M Citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K 2 VAPOR DIFFUSION, SITTING DROP 3.93 293 NANODROP, 0.86M Ammonium sulfate, 0.1M Citrate pH 3.93, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.252 α = 90 b = 57.252 β = 90 c = 147.151 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 2007-08-30 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-06-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0000 ALS 8.2.2 2 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97925, 0.97895 SSRL BL11-1
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 2.12 45.175 99.1 0.066 16.76 14544 -3 56.283
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 2.12 2.2 99.7 0.61 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.12 45.175 14517 699 99.37 0.217 0.215 0.22 0.251 0.2657 RANDOM 49.003
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] 1.79 1.79 -3.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.026 r_dihedral_angle_4_deg 16.475 r_dihedral_angle_3_deg 16.36 r_scangle_it 8.748 r_scbond_it 5.965 r_dihedral_angle_1_deg 5.093 r_mcangle_it 3.537 r_mcbond_it 2.409 r_angle_refined_deg 1.69 r_angle_other_deg 0.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.026 r_dihedral_angle_4_deg 16.475 r_dihedral_angle_3_deg 16.36 r_scangle_it 8.748 r_scbond_it 5.965 r_dihedral_angle_1_deg 5.093 r_mcangle_it 3.537 r_mcbond_it 2.409 r_angle_refined_deg 1.69 r_angle_other_deg 0.971 r_mcbond_other 0.515 r_nbd_refined 0.229 r_symmetry_vdw_other 0.22 r_nbd_other 0.203 r_nbtor_refined 0.186 r_symmetry_hbond_refined 0.157 r_symmetry_vdw_refined 0.135 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.105 r_nbtor_other 0.095 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1349 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction ADSC data collection XDS data reduction SHELXD phasing autoSHARP phasing