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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 5.5 293 78mM sodium acetate, 0.44mM EDTA, 6.7mM DITHIOTHREITOL, 2.4% PEG 4000 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.212 α = 89.01 b = 97.016 β = 109.2 c = 109.494 γ = 100.21
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 MARMOSAIC 225 mm CCD mirror 2008-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.9786 EMBL/DESY, HAMBURG X12
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 20 94.1 0.089 12.55 1.99 88675 88675 -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 2.56 94.9 0.595 2.01 1.99 6634
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 19.64 84232 84232 4439 94.38 0.21755 0.21755 0.2152 0.2157 0.26166 0.2608 RANDOM 37.533
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] 0.03 0.01 -0.02 0.02 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.298 r_dihedral_angle_4_deg 18.081 r_dihedral_angle_3_deg 15.958 r_dihedral_angle_1_deg 6.157 r_scangle_it 1.472 r_angle_refined_deg 1.218 r_scbond_it 0.947 r_angle_other_deg 0.861 r_mcangle_it 0.538 r_mcbond_it 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.298 r_dihedral_angle_4_deg 18.081 r_dihedral_angle_3_deg 15.958 r_dihedral_angle_1_deg 6.157 r_scangle_it 1.472 r_angle_refined_deg 1.218 r_scbond_it 0.947 r_angle_other_deg 0.861 r_mcangle_it 0.538 r_mcbond_it 0.316 r_mcbond_other 0.138 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 17159 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 24
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling