2P0R

Structure of Human Calpain 9 in complex with Leupeptin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529114.7% Peg 8000, 10% glycerol, 0.1M Na-Cacodylate, 0.15M Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6954.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.165α = 90
b = 97.165β = 90
c = 173.378γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-01-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.5301000.0838.59.13314533145153.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5999.60.6462.63.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1NQA2.519.43278612786114911000.213210.210170.26889RANDOM35.859
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]
0.030.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.976
r_dihedral_angle_4_deg15.515
r_dihedral_angle_3_deg14.523
r_dihedral_angle_1_deg7.545
r_scangle_it1.81
r_angle_refined_deg1.385
r_scbond_it1.199
r_mcangle_it1.049
r_angle_other_deg0.901
r_mcbond_it0.621
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.976
r_dihedral_angle_4_deg15.515
r_dihedral_angle_3_deg14.523
r_dihedral_angle_1_deg7.545
r_scangle_it1.81
r_angle_refined_deg1.385
r_scbond_it1.199
r_mcangle_it1.049
r_angle_other_deg0.901
r_mcbond_it0.621
r_mcbond_other0.362
r_symmetry_vdw_other0.275
r_nbd_refined0.214
r_xyhbond_nbd_refined0.197
r_nbd_other0.193
r_nbtor_refined0.181
r_symmetry_hbond_refined0.158
r_metal_ion_refined0.127
r_symmetry_vdw_refined0.127
r_nbtor_other0.086
r_chiral_restr0.079
r_xyhbond_nbd_other0.076
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5162
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms5

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling