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The Structural Basis of Differential Inhibition of Human Calpain by Indole and Phenyl alpha-Mercaptoacrylic Acids
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PHJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 50 mM sodium cacodylate, 12.5% PEG6000, 20 mM calcium chloride and 10 mM DTT at pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.8 56.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.41 α = 90 b = 79.34 β = 91.23 c = 57.26 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 PIXEL DECTRIS PILATUS 2M 2013-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9673 Diamond I03
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 2.03 41.93 95 0.038 17.9 3.5 27196 27196
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 2.03 2.08 78.4 0.655 2.4 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4PHJ 2.03 41.93 25811 1360 94.92 0.19987 0.19716 0.25094 0.2372 RANDOM 44.789
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] -0.61 -0.76 -0.19 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.447 r_dihedral_angle_3_deg 18.143 r_dihedral_angle_4_deg 13.27 r_long_range_B_refined 7.532 r_long_range_B_other 7.468 r_dihedral_angle_1_deg 6.567 r_scangle_other 5.177 r_scbond_it 3.488 r_scbond_other 3.486 r_mcangle_it 3.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.447 r_dihedral_angle_3_deg 18.143 r_dihedral_angle_4_deg 13.27 r_long_range_B_refined 7.532 r_long_range_B_other 7.468 r_dihedral_angle_1_deg 6.567 r_scangle_other 5.177 r_scbond_it 3.488 r_scbond_other 3.486 r_mcangle_it 3.239 r_mcangle_other 3.238 r_mcbond_it 2.27 r_mcbond_other 2.268 r_angle_refined_deg 2.007 r_angle_other_deg 0.981 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2806 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing