2NQG

Calpain 1 proteolytic core inactivated by WR18(S,S), an epoxysuccinyl-type inhibitor.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G8JPDB entry 2G8J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298Expansion 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 coefficientSolvent content
2.0339.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.554α = 90
b = 70.588β = 90
c = 110.186γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC CONFOCAL MIRROR2006-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.04110.4388.10.07914.61745519.4
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)RedundancyNumber Unique Reflections (All)
2.042.1259.40.3250.3254.11848

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 REPLACEMENTTHROUGHOUTPDB entry 2G8J2.0423.11745592788.070.183740.18010.25118RANDOM18.387
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]
-0.510.340.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.727
r_dihedral_angle_4_deg17.962
r_dihedral_angle_3_deg16.211
r_dihedral_angle_1_deg7.207
r_scangle_it3.778
r_scbond_it2.515
r_mcangle_it1.756
r_angle_refined_deg1.675
r_mcbond_it1.085
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.727
r_dihedral_angle_4_deg17.962
r_dihedral_angle_3_deg16.211
r_dihedral_angle_1_deg7.207
r_scangle_it3.778
r_scbond_it2.515
r_mcangle_it1.756
r_angle_refined_deg1.675
r_mcbond_it1.085
r_nbtor_refined0.306
r_metal_ion_refined0.303
r_nbd_refined0.221
r_symmetry_vdw_refined0.218
r_symmetry_hbond_refined0.185
r_xyhbond_nbd_refined0.156
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.007
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 AtomsNumber
Protein Atoms2631
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing