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Calpain 1 proteolytic core inactivated by ZLAK-3001, 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 2.02 39.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.43 α = 90 b = 70.25 β = 90 c = 110.41 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 1.8 59.235 99.2 0.04 14.9 6.6 29716 29944
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 1.8 1.9 99.4 0.122 15.1 6.7
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 1.8 27.6 28210 28210 1505 99.24 0.15818 0.15613 0.1551 0.1957 0.1946 RANDOM 14.281
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] -0.2 0.24 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_dihedral_angle_4_deg 17.557 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_1_deg 6.497 r_scangle_it 3.902 r_scbond_it 2.46 r_mcangle_it 1.745 r_angle_refined_deg 1.467 r_mcbond_it 1.072 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_dihedral_angle_4_deg 17.557 r_dihedral_angle_3_deg 12.806 r_dihedral_angle_1_deg 6.497 r_scangle_it 3.902 r_scbond_it 2.46 r_mcangle_it 1.745 r_angle_refined_deg 1.467 r_mcbond_it 1.072 r_nbtor_refined 0.312 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.206 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.116 r_metal_ion_refined 0.081 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 305 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection MOSFLM data reduction SCALA data scaling MOLREP phasing