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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 1H2W PDB ENTRY 1H2W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 295 PEG 8000, Tris, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.341 α = 90 b = 91.224 β = 91 c = 79.787 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 QUANTUM 210 monochromator 2003-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 50 98.9 0.071 13 5.2 68648 68648 24.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 92.2 0.502 1.7 2.1 6381
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT PDB ENTRY 1H2W 1.8 30 66171 66171 3538 98.56 0.1622 0.16229 0.161 0.18614 RANDOM 15.553
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] -0.97 -0.13 1.93 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.281 r_scangle_it 4.352 r_scbond_it 2.764 r_mcangle_it 1.755 r_angle_refined_deg 1.561 r_angle_other_deg 1.026 r_mcbond_it 0.988 r_symmetry_vdw_other 0.301 r_nbd_other 0.262 r_nbd_refined 0.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.281 r_scangle_it 4.352 r_scbond_it 2.764 r_mcangle_it 1.755 r_angle_refined_deg 1.561 r_angle_other_deg 1.026 r_mcbond_it 0.988 r_symmetry_vdw_other 0.301 r_nbd_other 0.262 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.127 r_symmetry_vdw_refined 0.118 r_chiral_restr 0.101 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5251 Nucleic Acid Atoms Solvent Atoms 660 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing