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Calpain 1 proteolytic core inactivated by ZLAK-3002, an alpha-ketoamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KXR pdb entry 1kxr chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 1.5 M NaCl, 10 mM CaCl2, and 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.04 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.569 α = 90 b = 70.568 β = 90 c = 110.406 γ = 90
Symmetry Space Group P 21 21 21
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 210 mirrors 2007-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.0 NSLS X6A
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 1.6 59.46 96.6 0.078 8.4 5.6 42370 42370
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 1.6 1.69 82.6 0.602 1.6 3.1
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 pdb entry 1kxr chain A 1.6 35.29 40535 38914 2082 96.03 0.19057 0.18893 0.1871 0.22174 0.2187 RANDOM 15.802
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.311 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 12.095 r_dihedral_angle_1_deg 5.863 r_scangle_it 2.911 r_scbond_it 1.854 r_mcangle_it 1.379 r_angle_refined_deg 1.273 r_mcbond_it 0.838 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.311 r_dihedral_angle_4_deg 17.414 r_dihedral_angle_3_deg 12.095 r_dihedral_angle_1_deg 5.863 r_scangle_it 2.911 r_scbond_it 1.854 r_mcangle_it 1.379 r_angle_refined_deg 1.273 r_mcbond_it 0.838 r_nbtor_refined 0.309 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.177 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.126 r_metal_ion_refined 0.108 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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_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 2594 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection MOSFLM data reduction SCALA data scaling MOLREP phasing