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Crystal structure of a duf1185 family protein (spo0826) from silicibacter pomeroyi dss-3 at 2.10 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 NANODROP, 0.1M Sodium dihydrogen phosphate, 0.1M Potassium dihydrogen phosphate, 2.0M Sodium chloride, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.73 α = 90 b = 94.73 β = 90 c = 47.15 γ = 90
Symmetry Space Group P 43 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 2007-06-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162, 0.97922, 0.97905 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 2.1 27.308 99.3 0.038 15.82 13007 -3 51.74
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 2.1 2.17 98.2 0.717 2
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 2.1 27.308 12970 631 99.46 0.207 0.204 0.2029 0.259 0.2539 RANDOM 56.22
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] -0.05 -0.05 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.126 r_dihedral_angle_4_deg 20.623 r_dihedral_angle_3_deg 13.745 r_scangle_it 8.888 r_scbond_it 6.29 r_dihedral_angle_1_deg 4.527 r_mcangle_it 3.499 r_mcbond_it 2.166 r_angle_refined_deg 1.682 r_angle_other_deg 0.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.126 r_dihedral_angle_4_deg 20.623 r_dihedral_angle_3_deg 13.745 r_scangle_it 8.888 r_scbond_it 6.29 r_dihedral_angle_1_deg 4.527 r_mcangle_it 3.499 r_mcbond_it 2.166 r_angle_refined_deg 1.682 r_angle_other_deg 0.925 r_mcbond_other 0.489 r_symmetry_vdw_other 0.359 r_symmetry_hbond_refined 0.295 r_nbd_refined 0.208 r_nbd_other 0.201 r_symmetry_vdw_refined 0.179 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.142 r_nbtor_other 0.094 r_chiral_restr 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing SHARP phasing