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Structure and Catalysis of Acylaminoacyl Peptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HU5 Hydrolase and propeller domains of PDB entry 2HU5.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 170mM sodium acetate, 0.4mM EDTA, 10% dimethyl sulphoxide, 2.5% PEG 4000 , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.52 72.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.27 α = 90 b = 227.524 β = 100.37 c = 110.684 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MAR555 FLAT PANEL mirror 2009-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8148 EMBL/DESY, HAMBURG X11
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 30 96.8 0.092 11.43 3.3 149375 149375 -3
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 2.6 98.8 0.642 2.48 3.3 16732
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT Hydrolase and propeller domains of PDB entry 2HU5. 2.5 29.52 141856 141856 7519 96.89 0.20099 0.20099 0.19914 0.1965 0.23589 0.2297 RANDOM 35.233
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] -0.02 -0.02 0.11 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.229 r_dihedral_angle_4_deg 19.254 r_dihedral_angle_3_deg 15.887 r_dihedral_angle_1_deg 6.245 r_scangle_it 2.818 r_scbond_it 1.855 r_angle_refined_deg 1.748 r_angle_other_deg 1.12 r_mcangle_it 1.065 r_mcbond_it 0.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.229 r_dihedral_angle_4_deg 19.254 r_dihedral_angle_3_deg 15.887 r_dihedral_angle_1_deg 6.245 r_scangle_it 2.818 r_scbond_it 1.855 r_angle_refined_deg 1.748 r_angle_other_deg 1.12 r_mcangle_it 1.065 r_mcbond_it 0.642 r_mcbond_other 0.354 r_chiral_restr 0.097 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17452 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 33
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling