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Secreted aspartic protease 1 from Candida parapsilosis in complex with pepstatin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EAG PDB ENTRY 1EAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 five-fold molar inhibitor excess, Cpr=8mg/ml; drops: 0.002ml protein + 0.001ml reservoir + 0.0002ml 10mM ZnAc; reservoir: 0.1M Tris pH 7.0, 2.0M Ammonium Sulfate, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.79 55.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.488 α = 90 b = 194.247 β = 91.52 c = 97.147 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 SBC-3 2008-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.979 APS 19-BM
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 1.85 50 99.3 0.045 27.2 3.8 274936 273011
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 1.85 1.9 98.5 0.49 2.4 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EAG 1.85 46.03 252690 269660 1368 99.99 0.16646 0.16634 0.19014 0.2428 RANDOM 15.135
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] -2.83 0.37 0.57 2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.701 r_dihedral_angle_4_deg 16.49 r_dihedral_angle_3_deg 12.185 r_dihedral_angle_1_deg 6.015 r_scangle_it 2.544 r_scbond_it 1.635 r_angle_refined_deg 1.256 r_mcangle_it 1.023 r_mcbond_it 0.61 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.701 r_dihedral_angle_4_deg 16.49 r_dihedral_angle_3_deg 12.185 r_dihedral_angle_1_deg 6.015 r_scangle_it 2.544 r_scbond_it 1.635 r_angle_refined_deg 1.256 r_mcangle_it 1.023 r_mcbond_it 0.61 r_nbtor_refined 0.302 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.182 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 20582 Nucleic Acid Atoms Solvent Atoms 2159 Heterogen Atoms 225
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling