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Crystal structure of uncharacterized protein conserved in bacteria with a cystatin-like fold (YP_168589.1) from SILICIBACTER POMEROYI DSS-3 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.2000M MgCl2, 2.5000M NaCl, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.07 69.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.88 α = 90 b = 120.88 β = 90 c = 120.88 γ = 90
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 2008-12-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97982 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 28.49 99.1 0.072 11.95 19903 -3 30.973
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 96.2 0.866 1.4
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 28.49 19902 1018 99.87 0.177 0.176 0.1844 0.185 0.1979 RANDOM 48.955
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.327 r_dihedral_angle_4_deg 13.777 r_dihedral_angle_3_deg 10.35 r_scangle_it 4.501 r_dihedral_angle_1_deg 3.858 r_scbond_it 3.369 r_angle_refined_deg 1.711 r_mcangle_it 1.68 r_angle_other_deg 1.555 r_mcbond_it 1.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.327 r_dihedral_angle_4_deg 13.777 r_dihedral_angle_3_deg 10.35 r_scangle_it 4.501 r_dihedral_angle_1_deg 3.858 r_scbond_it 3.369 r_angle_refined_deg 1.711 r_mcangle_it 1.68 r_angle_other_deg 1.555 r_mcbond_it 1.188 r_symmetry_vdw_other 0.193 r_nbd_refined 0.156 r_mcbond_other 0.147 r_nbtor_refined 0.14 r_nbd_other 0.118 r_chiral_restr 0.098 r_xyhbond_nbd_refined 0.075 r_symmetry_vdw_refined 0.071 r_nbtor_other 0.066 r_symmetry_hbond_refined 0.059 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1113 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 4
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