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Crystal structure of a putative phosphosugar isomerase (sden_2705) from shewanella denitrificans os217 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.64 277 17.5000% polyethylene glycol 6000, 0.1M citric acid pH 4.64, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.56 51.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.579 α = 90 b = 89.445 β = 90 c = 109.497 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 collimating mirror, toroid focusing mirror 2009-01-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97961,0.97944 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 2 29.136 98.5 0.061 10.69 3.6 50053 -3 26.518
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 2.07 95.2 0.507 1.7
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 29.136 49992 2540 99.48 0.167 0.165 0.1718 0.203 0.2065 RANDOM 24.263
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] 0.4 0.21 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.101 r_dihedral_angle_3_deg 12.701 r_dihedral_angle_4_deg 11.595 r_scangle_it 7.42 r_scbond_it 5.306 r_dihedral_angle_1_deg 4.524 r_mcangle_it 3.053 r_mcbond_it 1.863 r_angle_refined_deg 1.526 r_angle_other_deg 0.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.101 r_dihedral_angle_3_deg 12.701 r_dihedral_angle_4_deg 11.595 r_scangle_it 7.42 r_scbond_it 5.306 r_dihedral_angle_1_deg 4.524 r_mcangle_it 3.053 r_mcbond_it 1.863 r_angle_refined_deg 1.526 r_angle_other_deg 0.981 r_mcbond_other 0.528 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4608 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 32
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