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Crystal structure of sugar phosphate isomerase from a cupin superfamily SPO2919 from Silicibacter pomeroyi (YP_168127.1) from SILICIBACTER POMEROYI DSS-3 at 2.30 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.33 277 24.0000% polyethylene glycol 8000, 0.3000M sodium acetate, 0.1M sodium cacodylate pH 6.33, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.815 α = 90 b = 52.815 β = 90 c = 252.163 γ = 90
Symmetry Space Group P 41 21 2
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 2009-01-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97959,0.97941 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 29.761 99.9 0.336 0.336 8.3 9.3 16869 23.149
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 99.7 0.012 1.204 0.6 9.5 1188
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 2.3 29.761 16826 850 99.75 0.198 0.196 0.2048 0.245 0.2155 RANDOM 32.484
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 0.4 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.215 r_dihedral_angle_3_deg 14.248 r_dihedral_angle_4_deg 12.146 r_dihedral_angle_1_deg 6.168 r_scangle_it 4.001 r_scbond_it 3.1 r_mcangle_it 2.081 r_mcbond_it 1.644 r_angle_refined_deg 1.369 r_angle_other_deg 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.215 r_dihedral_angle_3_deg 14.248 r_dihedral_angle_4_deg 12.146 r_dihedral_angle_1_deg 6.168 r_scangle_it 4.001 r_scbond_it 3.1 r_mcangle_it 2.081 r_mcbond_it 1.644 r_angle_refined_deg 1.369 r_angle_other_deg 0.886 r_mcbond_other 0.357 r_symmetry_vdw_other 0.311 r_symmetry_hbond_refined 0.224 r_nbd_other 0.201 r_nbd_refined 0.195 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.164 r_symmetry_vdw_refined 0.108 r_nbtor_other 0.085 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2378 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 22
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