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Prolyl tripeptidyl aminopeptidase mutant E636A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D5L PDB ENTRY 2D5L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 1.1M potassium sodium tartrate, 0.2M lithium sulfate, 0.1M CHES buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.27 62.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.709 α = 90 b = 149.709 β = 90 c = 160.943 γ = 120
Symmetry Space Group P 63 2 2
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 315 monochrometor 2006-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 50 99.9 0.064 81 20 71953 71953 31.5
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 2 2.07 99.6 0.314 11.6 19.1 7036
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2D5L 2 20 66242 66242 3533 97.01 0.18753 0.186 0.1863 0.21609 0.2166 RANDOM 36.773
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] -0.59 -0.29 -0.59 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.639 r_dihedral_angle_4_deg 16.622 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_1_deg 6.442 r_scangle_it 3.628 r_scbond_it 2.402 r_mcangle_it 1.561 r_angle_refined_deg 1.449 r_mcbond_it 0.989 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.639 r_dihedral_angle_4_deg 16.622 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_1_deg 6.442 r_scangle_it 3.628 r_scbond_it 2.402 r_mcangle_it 1.561 r_angle_refined_deg 1.449 r_mcbond_it 0.989 r_nbtor_refined 0.31 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.159 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5193 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling