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Crystal structure of a sugar phosphate isomerase/epimerase (BDI_3400) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.56 277 5.0% polyethylene glycol 1000, 32.9% Ethanol, 0.1M phosphate-citrate pH 4.56, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.26 45.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.745 α = 77.8 b = 48.69 β = 74.67 c = 79.88 γ = 68.9
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) 2009-12-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97910 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 27.437 87.3 0.045 10.89 64918 -3 17.188
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 80.8 0.252 2.2 1.99
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 27.437 64915 3301 96.24 0.141 0.1398 0.1519 0.1637 0.1804 RANDOM 24.0093
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] 0.72 -0.26 -0.5 -0.25 0.52 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.235 r_dihedral_angle_4_deg 16.836 r_dihedral_angle_3_deg 13.136 r_dihedral_angle_1_deg 6.416 r_scangle_it 3.8 r_scbond_it 2.43 r_angle_refined_deg 1.612 r_mcangle_it 1.611 r_angle_other_deg 1.229 r_mcbond_it 0.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.235 r_dihedral_angle_4_deg 16.836 r_dihedral_angle_3_deg 13.136 r_dihedral_angle_1_deg 6.416 r_scangle_it 3.8 r_scbond_it 2.43 r_angle_refined_deg 1.612 r_mcangle_it 1.611 r_angle_other_deg 1.229 r_mcbond_it 0.931 r_mcbond_other 0.284 r_chiral_restr 0.097 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4589 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 40
Software Software Software Name Purpose SOLVE phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction