4PHM

The Structural Basis of Differential Inhibition of Human Calpain by Indole and Phenyl alpha-Mercaptoacrylic Acids


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29350 mM sodium cacodylate, 12.5% PEG6000, 20 mM calcium chloride and 10 mM DTT at pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.856.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.41α = 90
b = 79.34β = 91.23
c = 57.26γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9673DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0341.93950.03817.93.52719627196
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.032.0878.40.6552.42.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4PHJ2.0341.9325811136094.920.199870.197160.25094RANDOM44.789
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]
-0.61-0.76-0.190.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.447
r_dihedral_angle_3_deg18.143
r_dihedral_angle_4_deg13.27
r_long_range_B_refined7.532
r_long_range_B_other7.468
r_dihedral_angle_1_deg6.567
r_scangle_other5.177
r_scbond_it3.488
r_scbond_other3.486
r_mcangle_it3.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.447
r_dihedral_angle_3_deg18.143
r_dihedral_angle_4_deg13.27
r_long_range_B_refined7.532
r_long_range_B_other7.468
r_dihedral_angle_1_deg6.567
r_scangle_other5.177
r_scbond_it3.488
r_scbond_other3.486
r_mcangle_it3.239
r_mcangle_other3.238
r_mcbond_it2.27
r_mcbond_other2.268
r_angle_refined_deg2.007
r_angle_other_deg0.981
r_chiral_restr0.125
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2806
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing