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High resolution crystal structure of cruzain bound to the vinyl sulfone inhibitor SMDC-256047
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1M Sodium HEPES pH 7.5, 2% PEG 400, 2.0M Ammonium sulfate, 30% Ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.18 43.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.687 α = 90 b = 72.493 β = 89.79 c = 60.93 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 ADSC QUANTUM 315r Vertical focusing mirror 2008-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.0 SSRL BL7-1
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 1.75 72.5 97.3 0.057 25 7.4 38177 38177 11.5
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 1.75 1.84 90 0.137 12 7.2 5147
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.75 60.93 36240 1918 97.15 0.14469 0.14297 0.1446 0.17636 0.1757 RANDOM 4.456
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] 0.37 0.04 -0.01 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.64 r_dihedral_angle_4_deg 20.45 r_dihedral_angle_3_deg 10.268 r_dihedral_angle_1_deg 6.137 r_scangle_it 3.515 r_scbond_it 2.238 r_angle_refined_deg 1.588 r_mcangle_it 1.355 r_angle_other_deg 0.976 r_mcbond_it 0.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.64 r_dihedral_angle_4_deg 20.45 r_dihedral_angle_3_deg 10.268 r_dihedral_angle_1_deg 6.137 r_scangle_it 3.515 r_scbond_it 2.238 r_angle_refined_deg 1.588 r_mcangle_it 1.355 r_angle_other_deg 0.976 r_mcbond_it 0.864 r_mcbond_other 0.284 r_chiral_restr 0.1 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3175 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 98
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling