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Calpain 1 proteolytic core in complex with SNJ-1715, a cyclic hemiacetal-type inhibitor
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 6.25 298 1.4 M NaCl, 10 mM CaCl2, 0.1 M MES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.78 55.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.542 α = 90 b = 85.542 β = 90 c = 117.946 γ = 90
Symmetry Space Group P 43 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH OSMIC CONFOCAL MIRROR SYSTEM 2005-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.249 19.57 96.7 0.084 0.084 7.9 7.6 21383 32.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.35 96.7 0.364 0.364 2 7.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1KXR, CHAIN A 2.25 19.57 21496 21382 1097 99.5 0.181 0.177 0.244 0.2265 RANDOM 26.5
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] -0.8 -0.8 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.416 r_dihedral_angle_3_deg 17.02 r_dihedral_angle_4_deg 16.596 r_dihedral_angle_1_deg 6.523 r_scangle_it 4.29 r_scbond_it 2.895 r_mcangle_it 1.882 r_angle_refined_deg 1.753 r_mcbond_it 1.157 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.416 r_dihedral_angle_3_deg 17.02 r_dihedral_angle_4_deg 16.596 r_dihedral_angle_1_deg 6.523 r_scangle_it 4.29 r_scbond_it 2.895 r_mcangle_it 1.882 r_angle_refined_deg 1.753 r_mcbond_it 1.157 r_nbtor_refined 0.309 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.201 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.126 r_metal_ion_refined 0.11 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_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 2626 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 38
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection CCP4 data scaling