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Crystal Structure of Falcipain-2 with Its inhibitor, E64
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YVB PDB ENTRY 1YVB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 100 mM Sodium Citrate, 10% PEG 3350, 100 mM Magnesium Formate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.93 75.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.778 α = 90 b = 167.81 β = 90 c = 177.758 γ = 90
Symmetry Space Group C 2 2 21
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 2006-03-08 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 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 2.83 66.7 99.3 0.201 10.04 7.3 45440 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 2.83 2.99 96.5 0.653 1.22 7.04
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 1YVB 2.9 66.67 45440 2418 99.9 0.27794 0.27546 0.2754 0.32542 0.3228 RANDOM 66.289
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] 0.58 -1.22 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.34 r_dihedral_angle_3_deg 15.389 r_dihedral_angle_4_deg 10.928 r_dihedral_angle_1_deg 6.458 r_angle_refined_deg 1.049 r_angle_other_deg 0.812 r_scangle_it 0.709 r_scbond_it 0.54 r_mcangle_it 0.419 r_mcbond_it 0.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.34 r_dihedral_angle_3_deg 15.389 r_dihedral_angle_4_deg 10.928 r_dihedral_angle_1_deg 6.458 r_angle_refined_deg 1.049 r_angle_other_deg 0.812 r_scangle_it 0.709 r_scbond_it 0.54 r_mcangle_it 0.419 r_mcbond_it 0.358 r_nbd_refined 0.205 r_nbtor_refined 0.184 r_nbd_other 0.177 r_symmetry_vdw_other 0.174 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_refined 0.145 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_other 0.086 r_nbtor_other 0.084 r_chiral_restr 0.062 r_mcbond_other 0.035 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 7305 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction XSCALE data scaling PHASER phasing