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Crystal structure of Sugar phosphate isomerase/epimerase (YP_001303399.1) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 277 0.2000M MgAcetate, 20.0000% PEG-3350, No Buffer pH 7.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.657 α = 90 b = 56.634 β = 102.98 c = 78.188 γ = 90
Symmetry Space Group C 1 2 1
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) 2009-07-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97935 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 1.7 28.318 96.3 0.045 9.45 2.81 36149 -3 19.269
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 1.7 1.76 92.7 0.339 1.97
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 1.7 28.318 36149 1806 99.07 0.149 0.148 0.1576 0.167 0.1761 RANDOM 34.044
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] -0.01 0.22 1.51 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.251 r_dihedral_angle_3_deg 12.562 r_dihedral_angle_4_deg 12.353 r_dihedral_angle_1_deg 5.299 r_scangle_it 3.062 r_scbond_it 2.375 r_angle_refined_deg 1.557 r_mcangle_it 1.385 r_mcbond_it 1.031 r_angle_other_deg 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.251 r_dihedral_angle_3_deg 12.562 r_dihedral_angle_4_deg 12.353 r_dihedral_angle_1_deg 5.299 r_scangle_it 3.062 r_scbond_it 2.375 r_angle_refined_deg 1.557 r_mcangle_it 1.385 r_mcbond_it 1.031 r_angle_other_deg 1.02 r_symmetry_hbond_refined 0.257 r_mcbond_other 0.255 r_symmetry_vdw_other 0.218 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.183 r_nbd_other 0.175 r_symmetry_vdw_refined 0.139 r_nbtor_other 0.088 r_chiral_restr 0.08 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_metal_ion_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2185 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction