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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 4.5 293 78mM sodium acetate, 0.44mM EDTA, 6.7mM dithiothreitol, 2.0% PEG 4000 , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.44 72.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.63 α = 90 b = 209.89 β = 90 c = 205.92 γ = 90
Symmetry Space Group C 2 2 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 MAR CCD 165 mm mirrors 2008-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.9999 ELETTRA 5.2R
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 2.7 20 99.3 0.094 13.2 5.94 61532 61532 -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) 2.7 2.77 99.8 0.527 3.3 6.26 4545
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-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. 2.7 19.8 58407 58407 3091 99.63 0.20934 0.20934 0.2071 0.25192 0.255 RANDOM 43.197
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] 0.18 -0.1 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.464 r_dihedral_angle_4_deg 21.663 r_dihedral_angle_3_deg 16.576 r_dihedral_angle_1_deg 6.414 r_scangle_it 3.065 r_scbond_it 1.938 r_angle_refined_deg 1.734 r_angle_other_deg 1.24 r_mcangle_it 1.123 r_mcbond_it 0.637
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.464 r_dihedral_angle_4_deg 21.663 r_dihedral_angle_3_deg 16.576 r_dihedral_angle_1_deg 6.414 r_scangle_it 3.065 r_scbond_it 1.938 r_angle_refined_deg 1.734 r_angle_other_deg 1.24 r_mcangle_it 1.123 r_mcbond_it 0.637 r_mcbond_other 0.267 r_chiral_restr 0.097 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 8568 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 37
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling