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Crystal structure of Putative sugar isomerase. (YP_001305105.1) from Parabacteroides distasonis ATCC 8503 at 1.44 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.57 277 19.5000% polyethylene glycol 3000, 0.1M citric acid pH 5.57, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.6 52.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.594 α = 90 b = 81.906 β = 90 c = 95.485 γ = 90
Symmetry Space Group C 2 2 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 collimating mirror, toroid focusing mirror 2009-11-06 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97944,0.97932 SSRL BL9-2
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 1.44 28.355 76.7 0.053 10.02 47272 -3 17.141
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 1.44 1.49 79 0.49 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 1.44 28.355 47252 2401 84.51 0.151 0.149 0.1559 0.185 0.1883 RANDOM 19.044
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] -0.63 0.96 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.271 r_dihedral_angle_4_deg 14.498 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_1_deg 5.726 r_scangle_it 5.49 r_scbond_it 4.069 r_mcangle_it 2.104 r_mcbond_it 1.763 r_angle_refined_deg 1.688 r_angle_other_deg 0.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.271 r_dihedral_angle_4_deg 14.498 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_1_deg 5.726 r_scangle_it 5.49 r_scbond_it 4.069 r_mcangle_it 2.104 r_mcbond_it 1.763 r_angle_refined_deg 1.688 r_angle_other_deg 0.979 r_mcbond_other 0.457 r_symmetry_vdw_refined 0.27 r_symmetry_vdw_other 0.262 r_nbd_refined 0.245 r_nbd_other 0.193 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.107 r_nbtor_other 0.086 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2003 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction