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Calpain 1 proteolytic core inactivated by WR13(R,R), an epoxysuccinyl-type inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G8J PDB entry 2G8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 Expansion around 1.1-1.7 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 39.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.369 α = 90 b = 70.06 β = 90 c = 110.743 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 IMAGE PLATE MARRESEARCH OSMIC CONFOCAL MIRROR 2006-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 2.04 59.3 99.3 0.139 11 19556 17.3
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) 2.04 2.12 72.4 0.456 3.1 2235
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 2G8J 2.04 59.23 15556 1057 99.34 0.1841 0.18066 0.1807 0.24735 0.2423 RANDOM 16.674
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] -0.06 0.07 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.553 r_dihedral_angle_4_deg 20.481 r_dihedral_angle_3_deg 14.988 r_dihedral_angle_1_deg 6.689 r_scangle_it 3.684 r_scbond_it 2.53 r_mcangle_it 1.762 r_angle_refined_deg 1.659 r_mcbond_it 1.088 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.553 r_dihedral_angle_4_deg 20.481 r_dihedral_angle_3_deg 14.988 r_dihedral_angle_1_deg 6.689 r_scangle_it 3.684 r_scbond_it 2.53 r_mcangle_it 1.762 r_angle_refined_deg 1.659 r_mcbond_it 1.088 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.283 r_symmetry_hbond_refined 0.281 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.121 r_metal_ion_refined 0.081 r_bond_refined_d 0.017 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 2634 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing