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Crystal Structure of Probable Thioesterase from Bartonella henselae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PZH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 Sparse matrix screen condition a9, 20% PEG 3350, 0.2 M ammonium chloride,
16 mg/mL protein, crystal tracking ID 202329a9, 0.1 mg/mL chymotrypsin, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.73 28.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.639 α = 90 b = 87.853 β = 90 c = 96.91 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 ADSC QUANTUM 315 2009-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.9765 ALS 5.0.3
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 2.5 50 99.4 0.121 13.5 5.7 18932
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) 2.5 2.59 96.9 0.464 2.25 4 1787
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 2PZH 2.5 40.01 18726 952 98.25 0.209 0.206 0.2064 0.268 0.2021 RANDOM 37.346
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] 0.5 -2.19 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.377 r_dihedral_angle_4_deg 17.625 r_dihedral_angle_3_deg 17.466 r_dihedral_angle_1_deg 6.588 r_scangle_it 3.018 r_scbond_it 1.764 r_mcangle_it 1.454 r_angle_refined_deg 1.313 r_mcbond_it 0.774 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.377 r_dihedral_angle_4_deg 17.625 r_dihedral_angle_3_deg 17.466 r_dihedral_angle_1_deg 6.588 r_scangle_it 3.018 r_scbond_it 1.764 r_mcangle_it 1.454 r_angle_refined_deg 1.313 r_mcbond_it 0.774 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3909 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling