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Crystal Structure of the putative alpha/beta hydrolase RutD from E.coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 0.15 M Malic acid 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.597 α = 90 b = 79.597 β = 90 c = 161.753 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 225 mm CCD 2010-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 2.1 50 98 0.352 0.352 11.6 10.2 31045 31045 -3 25.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 95 2.9 8.4 1451
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 2.1 50 28021 28021 1471 94.57 0.17188 0.17188 0.16915 0.1821 0.22565 0.2314 RANDOM 31.907
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] -0.14 -0.14 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.055 r_dihedral_angle_4_deg 21.201 r_dihedral_angle_3_deg 14.439 r_dihedral_angle_1_deg 5.649 r_angle_other_deg 4.291 r_angle_refined_deg 1.492 r_chiral_restr 0.077 r_bond_refined_d 0.013 r_gen_planes_other 0.009 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.055 r_dihedral_angle_4_deg 21.201 r_dihedral_angle_3_deg 14.439 r_dihedral_angle_1_deg 5.649 r_angle_other_deg 4.291 r_angle_refined_deg 1.492 r_chiral_restr 0.077 r_bond_refined_d 0.013 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4044 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 33
Software Software Software Name Purpose MD2 data collection HKL-3000 phasing SHELXCD phasing SHELXE model building MLPHARE phasing DM model building ARP/wARP model building SOLVE phasing RESOLVE model building CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling DM phasing RESOLVE phasing CCP4 phasing