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CRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM DUF3478 FAMILY WITH A SPOIIAA-LIKE FOLD (SHEW_3102) FROM SHEWANELLA LOIHICA PV-4 AT 2.25 A RESOLUTION
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.33 277 NANODROP, 0.2M Sodium chloride, 37.0% 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.33, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.63 53.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.387 α = 90 b = 113.963 β = 90 c = 130.692 γ = 90
Symmetry Space Group C 2 2 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 325 mm CCD Flat mirror (vertical focusing) 2007-05-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97926, 0.97895 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 2.25 28.653 99 0.067 0.067 17.89 7.2 14575 41.73
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 2.25 2.31 100 0.467 0.467 3.6 7 1060
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 2.25 28.653 14570 754 98.78 0.184 0.181 0.1878 0.239 0.2354 RANDOM 48.526
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] 3.53 0.8 -4.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_4_deg 13.08 r_dihedral_angle_3_deg 11.555 r_scangle_it 7.995 r_scbond_it 5.703 r_dihedral_angle_1_deg 4.09 r_mcangle_it 2.845 r_angle_refined_deg 1.756 r_mcbond_it 1.684 r_angle_other_deg 0.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_4_deg 13.08 r_dihedral_angle_3_deg 11.555 r_scangle_it 7.995 r_scbond_it 5.703 r_dihedral_angle_1_deg 4.09 r_mcangle_it 2.845 r_angle_refined_deg 1.756 r_mcbond_it 1.684 r_angle_other_deg 0.871 r_mcbond_other 0.605 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.194 r_symmetry_vdw_other 0.182 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.174 r_metal_ion_refined 0.168 r_nbd_other 0.158 r_chiral_restr 0.093 r_nbtor_other 0.09 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1937 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing autoSHARP phasing