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Structural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Inter-Domain Dynamics in Catalysis and Specificity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QFS PDB ENTRY 1QFS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 26% METHOXY PEG 5K AND 0.1MES (PH 6.01).
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.692 α = 90 b = 114.718 β = 103.6 c = 99.279 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC CCD 2003-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
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 1.5 50 98.9 0.07 12.8 4.1 225366 15.3
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 1.5 1.55 97.7 0.47 2.8 4
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 PDB ENTRY 1QFS 1.5 30 214057 11252 98.9 0.161 0.16 0.168 0.182 0.1886 RANDOM 10.34
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] -0.57 -0.01 0.47 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.16 r_scangle_it 3.114 r_mcangle_it 2.385 r_scbond_it 2.342 r_angle_refined_deg 1.491 r_mcbond_it 1.432 r_angle_other_deg 1.235 r_symmetry_vdw_other 0.311 r_nbd_other 0.257 r_nbd_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.16 r_scangle_it 3.114 r_mcangle_it 2.385 r_scbond_it 2.342 r_angle_refined_deg 1.491 r_mcbond_it 1.432 r_angle_other_deg 1.235 r_symmetry_vdw_other 0.311 r_nbd_other 0.257 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.133 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.111 r_nbtor_other 0.085 r_symmetry_vdw_refined 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10717 Nucleic Acid Atoms Solvent Atoms 1371 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing