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Crystal structure of Putative pectinase (YP_001304412.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 40.0000% Ethanol, 0.1170M magnesium chloride, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.116 α = 90 b = 104.606 β = 90 c = 393.587 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2009-07-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97926,0.97882 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 2.3 49.507 97.3 0.114 8.64 186629 -3 37.716
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 2.3 2.38 90.9 0.663 1.8
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 2.3 49.507 186512 9370 97.48 0.246 0.244 0.2529 0.28 0.2896 RANDOM 38.194
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] -1.62 1.86 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.23 r_dihedral_angle_3_deg 8.996 r_dihedral_angle_4_deg 8.005 r_scangle_it 4.424 r_dihedral_angle_1_deg 3.413 r_scbond_it 2.724 r_mcangle_it 1.438 r_angle_refined_deg 0.77 r_mcbond_it 0.711 r_angle_other_deg 0.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.23 r_dihedral_angle_3_deg 8.996 r_dihedral_angle_4_deg 8.005 r_scangle_it 4.424 r_dihedral_angle_1_deg 3.413 r_scbond_it 2.724 r_mcangle_it 1.438 r_angle_refined_deg 0.77 r_mcbond_it 0.711 r_angle_other_deg 0.517 r_mcbond_other 0.201 r_chiral_restr 0.062 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28340 Nucleic Acid Atoms Solvent Atoms 850 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing