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Crystal structure of a putative endoribonuclease (so_1960) from shewanella oneidensis mr-1 at 1.85 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 NANODROP, 0.16M Ca(OAc)2, 20.0% Glycerol, 14.4% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.71 54.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.083 α = 90 b = 62.908 β = 93.24 c = 78.689 γ = 90
Symmetry Space Group C 1 2 1
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 mirror (vertical focusing) 2007-01-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97931, 0.97885 SSRL BL11-1
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 1.85 29.21 100 0.105 0.105 5.9 3.8 46806 19.11
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 1.85 1.9 100 0.667 0.667 1.1 3.8 3463
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 (All) 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 1.85 29.21 46806 2366 99.95 0.152 0.152 0.151 0.1593 0.177 0.1858 RANDOM 19.687
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] 0.21 -0.17 1.02 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.977 r_dihedral_angle_4_deg 15.382 r_dihedral_angle_3_deg 12.795 r_scangle_it 6.541 r_dihedral_angle_1_deg 6.259 r_scbond_it 4.462 r_mcangle_it 2.49 r_angle_refined_deg 1.484 r_mcbond_it 1.394 r_angle_other_deg 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.977 r_dihedral_angle_4_deg 15.382 r_dihedral_angle_3_deg 12.795 r_scangle_it 6.541 r_dihedral_angle_1_deg 6.259 r_scbond_it 4.462 r_mcangle_it 2.49 r_angle_refined_deg 1.484 r_mcbond_it 1.394 r_angle_other_deg 0.96 r_symmetry_vdw_refined 0.737 r_mcbond_other 0.358 r_symmetry_vdw_other 0.343 r_symmetry_metal_ion_refined 0.251 r_nbd_refined 0.204 r_nbd_other 0.2 r_nbtor_refined 0.177 r_metal_ion_refined 0.17 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.159 r_chiral_restr 0.091 r_nbtor_other 0.088 r_bond_refined_d 0.015 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 3448 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 34
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling SHELXD phasing autoSHARP phasing