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Crystal structure of IroE-like serine hydrolase (NP_718593.1) from SHEWANELLA ONEIDENSIS at 2.12 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 15.0000% Ethanol, 0.2000M MgCl2, 0.1M Imidazole pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.65 α = 90 b = 125.57 β = 117.94 c = 56.75 γ = 90
Symmetry Space Group P 1 21 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) 2008-11-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162,0.97824,0.97864 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 2.12 28.307 79 0.058 8.62 33406 -3 25.019
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 2.12 2.2 77.9 0.276 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 2.12 28.307 33377 1684 88.55 0.187 0.184 0.1885 0.241 0.2422 RANDOM 25.264
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] 0.96 -0.14 -0.09 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.71 r_dihedral_angle_4_deg 13.952 r_dihedral_angle_3_deg 13.858 r_dihedral_angle_1_deg 3.62 r_angle_refined_deg 1.614 r_scangle_it 1.457 r_mcangle_it 1.416 r_scbond_it 1.007 r_angle_other_deg 0.99 r_mcbond_it 0.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.71 r_dihedral_angle_4_deg 13.952 r_dihedral_angle_3_deg 13.858 r_dihedral_angle_1_deg 3.62 r_angle_refined_deg 1.614 r_scangle_it 1.457 r_mcangle_it 1.416 r_scbond_it 1.007 r_angle_other_deg 0.99 r_mcbond_it 0.982 r_symmetry_vdw_other 0.358 r_mcbond_other 0.276 r_nbd_refined 0.215 r_nbd_other 0.2 r_symmetry_vdw_refined 0.189 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.183 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.101 r_nbtor_other 0.089 r_bond_refined_d 0.016 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 4985 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction