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Crystal structure of had family hydrolase t0658 from Salmonella enterica subsp. enterica serovar Typhi (Target EFI-501419)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P96
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1M SODIUM CACODYLATE, PH 6.5, 1M SODIUM CITRATE TRIBASIC, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.89 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.634 α = 90 b = 117.634 β = 90 c = 118.815 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 315 MIRRORS 2012-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.27 70 100 0.093 8.7 15.9 39163 -5 57.451
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.27 2.3 99.8 0.96 2 13.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3P96 2.27 41.62 37774 1221 99.63 0.19402 0.19227 0.1956 0.24631 0.2535 RANDOM 60.572
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] 1.42 1.42 -2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.523 r_dihedral_angle_4_deg 20.989 r_dihedral_angle_3_deg 16.49 r_dihedral_angle_1_deg 5.827 r_angle_refined_deg 1.31 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.523 r_dihedral_angle_4_deg 20.989 r_dihedral_angle_3_deg 16.49 r_dihedral_angle_1_deg 5.827 r_angle_refined_deg 1.31 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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 4600 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 4
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling