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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 2.48 50.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.405 α = 105.69 b = 97.979 β = 103.52 c = 98.797 γ = 100.36
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 2009-12-11 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 1.82 30 95.2 0.028 22.72 1.88 206854 206854 -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) 1.82 1.87 94.1 0.606 2.26 1.88 15188
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. 1.82 24.62 196431 196431 10388 95.29 0.20468 0.20468 0.20314 0.2084 0.23366 0.2379 RANDOM 36.26
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 0.04 0.09 0.06 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.218 r_dihedral_angle_4_deg 21.006 r_dihedral_angle_3_deg 15.42 r_dihedral_angle_1_deg 6.335 r_scangle_it 2.924 r_scbond_it 2.026 r_angle_refined_deg 1.722 r_angle_other_deg 1.426 r_mcangle_it 1.157 r_mcbond_it 0.775
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.218 r_dihedral_angle_4_deg 21.006 r_dihedral_angle_3_deg 15.42 r_dihedral_angle_1_deg 6.335 r_scangle_it 2.924 r_scbond_it 2.026 r_angle_refined_deg 1.722 r_angle_other_deg 1.426 r_mcangle_it 1.157 r_mcbond_it 0.775 r_mcbond_other 0.483 r_chiral_restr 0.098 r_bond_refined_d 0.019 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 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 17118 Nucleic Acid Atoms Solvent Atoms 928 Heterogen Atoms 32
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling