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Crystal Structure of Falcipain-3 with Its inhibitor, Leupeptin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BPF PDB ENTRY 3BPF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.015 M Magnesium Acetate, 50 mM Sodium cacodylate, 1.3 M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.57 α = 90 b = 154.57 β = 90 c = 129.011 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 315 mirrors 2007-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 92.85 100 0.091 0.023 27 15.9 20625
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 100 0.507 0.124 7.1 16.3
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 3BPF 2.5 92.85 20625 19568 1056 99.98 0.19138 0.18959 0.22423 0.2308 RANDOM 29.7
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] -0.16 -0.08 -0.16 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.537 r_dihedral_angle_3_deg 16.086 r_dihedral_angle_4_deg 15.962 r_dihedral_angle_1_deg 6.715 r_scangle_it 2.259 r_angle_refined_deg 1.549 r_scbond_it 1.536 r_mcangle_it 0.937 r_angle_other_deg 0.91 r_mcbond_it 0.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.537 r_dihedral_angle_3_deg 16.086 r_dihedral_angle_4_deg 15.962 r_dihedral_angle_1_deg 6.715 r_scangle_it 2.259 r_angle_refined_deg 1.549 r_scbond_it 1.536 r_mcangle_it 0.937 r_angle_other_deg 0.91 r_mcbond_it 0.693 r_symmetry_vdw_other 0.241 r_nbd_refined 0.211 r_nbd_other 0.202 r_nbtor_refined 0.195 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.153 r_mcbond_other 0.131 r_nbtor_other 0.095 r_symmetry_vdw_refined 0.089 r_chiral_restr 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3815 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling PHASER phasing