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Crystal structure of cruzain bound to an alpha-ketoester
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AIM cruzipain coordinate set 1AIM, without inhibitor or water molecules
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 0.6-1M NaCitrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.96 36.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.72 α = 90 b = 50.675 β = 116.74 c = 45.576 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 298 IMAGE PLATE RIGAKU RAXIS II Yale MSC mirrors 2000-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.3 40.82 0.092 5.1 7826 7826
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) 2.3 2.37 88.2 0.207 2.5
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 MOLECULAR REPLACEMENT THROUGHOUT cruzipain coordinate set 1AIM, without inhibitor or water molecules 2.3 40.82 7826 7457 363 93.32 0.13627 0.13224 0.1334 0.21773 0.2199 RANDOM 14.744
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] 0.05 -0.73 0.09 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.413 r_dihedral_angle_4_deg 19.529 r_dihedral_angle_3_deg 15.443 r_dihedral_angle_1_deg 6.616 r_scangle_it 4.223 r_scbond_it 2.669 r_angle_refined_deg 1.876 r_mcangle_it 1.599 r_mcbond_it 0.988 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.413 r_dihedral_angle_4_deg 19.529 r_dihedral_angle_3_deg 15.443 r_dihedral_angle_1_deg 6.616 r_scangle_it 4.223 r_scbond_it 2.669 r_angle_refined_deg 1.876 r_mcangle_it 1.599 r_mcbond_it 0.988 r_nbtor_refined 0.314 r_nbd_refined 0.276 r_symmetry_vdw_refined 0.273 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.177 r_chiral_restr 0.109 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1592 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 30
Software Software Software Name Purpose SCALEPACK data scaling X-PLOR model building REFMAC refinement X-PLOR phasing