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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 1ALV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PROTEIN WAS CRYSTALLIZED FROM 12% PEG6000, 20 MM CACL2, 50 MM CACODYLATE BUFFER, PH7.4
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.53 α = 90 b = 70.56 β = 108.79 c = 58.67 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 2013-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 1.79 39.05 98.4 0.041 16.6 3.7 35505 35505
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 1.79 1.84 99.9 0.622 2.1 3.9
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 1ALV 1.79 39.05 33708 1777 98.28 0.18577 0.18348 0.191 0.22826 0.2312 RANDOM 31.919
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 -0.7 -0.68 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.239 r_dihedral_angle_3_deg 16.637 r_dihedral_angle_4_deg 16.484 r_long_range_B_refined 6.381 r_long_range_B_other 6.319 r_dihedral_angle_1_deg 5.36 r_scangle_other 3.533 r_mcangle_it 2.495 r_mcangle_other 2.494 r_scbond_it 2.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.239 r_dihedral_angle_3_deg 16.637 r_dihedral_angle_4_deg 16.484 r_long_range_B_refined 6.381 r_long_range_B_other 6.319 r_dihedral_angle_1_deg 5.36 r_scangle_other 3.533 r_mcangle_it 2.495 r_mcangle_other 2.494 r_scbond_it 2.325 r_scbond_other 2.319 r_angle_refined_deg 2.008 r_mcbond_other 1.684 r_mcbond_it 1.683 r_angle_other_deg 1.085 r_chiral_restr 0.156 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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 2790 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing