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Crystal structure of putative phosphosugar isomerase (YP_167080.1) from SILICIBACTER POMEROYI DSS-3 at 1.75 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 277 0.2000M MgCl2, 20.0000% PEG-3350, No Buffer pH 5.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.02 39.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.4 α = 90 b = 114.141 β = 90 c = 197.279 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 300 mm CCD Adjustable focusing mirrors in K-B geometry 2008-10-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.94645,0.97967 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.75 29.386 98.1 0.115 0.115 0.128 9.4 4.3 117679 16.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 83.4 0.596 0.596 0.707 1.2 2.7 7290
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 1.75 29.386 117606 5897 97.9 0.164 0.162 0.1686 0.195 0.1993 RANDOM 14.586
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] 0.46 -0.44 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.094 r_dihedral_angle_4_deg 15.2 r_dihedral_angle_3_deg 11.398 r_dihedral_angle_1_deg 4.061 r_angle_refined_deg 1.528 r_scangle_it 1.306 r_mcangle_it 1.164 r_angle_other_deg 1.042 r_scbond_it 0.868 r_mcbond_it 0.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.094 r_dihedral_angle_4_deg 15.2 r_dihedral_angle_3_deg 11.398 r_dihedral_angle_1_deg 4.061 r_angle_refined_deg 1.528 r_scangle_it 1.306 r_mcangle_it 1.164 r_angle_other_deg 1.042 r_scbond_it 0.868 r_mcbond_it 0.752 r_symmetry_vdw_other 0.269 r_symmetry_hbond_refined 0.238 r_nbd_refined 0.218 r_mcbond_other 0.205 r_nbd_other 0.192 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.17 r_chiral_restr 0.096 r_nbtor_other 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9647 Nucleic Acid Atoms Solvent Atoms 1212 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing