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Crystal structure of a duf1696 family protein with a pleckstrin-homology domain (shew_0819) from shewanella loihica pv-4 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.83 277 37.0% 2-methyl-2,4-pentanediol, 0.15M sodium chloride, 0.1M HEPES pH 6.83, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.07 α = 90 b = 75.32 β = 90 c = 139.4 γ = 90
Symmetry Space Group P 21 21 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) 2008-04-10 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97925,0.91837,0.97871 SSRL BL11-1
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 29.828 97.9 0.056 11.19 4.05 43831 -3 31.07
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 95.9 0.638 1.5
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 29.828 43782 2200 98.93 0.186 0.184 0.1861 0.227 0.2288 RANDOM 25.932
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] 0.86 -0.94 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.851 r_dihedral_angle_4_deg 15.15 r_dihedral_angle_3_deg 14.384 r_scangle_it 6.697 r_dihedral_angle_1_deg 6.206 r_scbond_it 4.88 r_mcangle_it 2.667 r_mcbond_it 1.993 r_angle_refined_deg 1.413 r_angle_other_deg 0.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.851 r_dihedral_angle_4_deg 15.15 r_dihedral_angle_3_deg 14.384 r_scangle_it 6.697 r_dihedral_angle_1_deg 6.206 r_scbond_it 4.88 r_mcangle_it 2.667 r_mcbond_it 1.993 r_angle_refined_deg 1.413 r_angle_other_deg 0.895 r_mcbond_other 0.722 r_symmetry_vdw_other 0.221 r_symmetry_hbond_refined 0.214 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.198 r_nbd_other 0.194 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.16 r_nbtor_other 0.084 r_chiral_restr 0.079 r_bond_refined_d 0.014 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 4366 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 57
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