5N71

CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICINUS (IRCD1)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291CRYSTALLIZATION CONDITIONS: 1:1 PROTEIN (6 MG/ML IN 2 MM BIS-TRIS, PH 6.5, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.6, 30% PEG2000 MME), CRYOCOOLED IN MOTHER LIQUOR, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Crystal Properties
Matthews coefficientSolvent content
2.9958.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.156α = 90
b = 98.156β = 90
c = 90.795γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252015-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918410BESSY14.2

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
11.8849.0899.60.08516.167.9836745-3
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)
11.881.99980.9482.33

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.8849.0834906183899.660.199330.197990.22441RANDOM32.146
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]
0.070.07-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.336
r_dihedral_angle_4_deg16.664
r_dihedral_angle_3_deg13.961
r_dihedral_angle_1_deg6.89
r_long_range_B_refined5.836
r_long_range_B_other5.835
r_scangle_other4.548
r_mcangle_other3.811
r_mcangle_it3.807
r_scbond_it2.957
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.336
r_dihedral_angle_4_deg16.664
r_dihedral_angle_3_deg13.961
r_dihedral_angle_1_deg6.89
r_long_range_B_refined5.836
r_long_range_B_other5.835
r_scangle_other4.548
r_mcangle_other3.811
r_mcangle_it3.807
r_scbond_it2.957
r_scbond_other2.957
r_mcbond_it2.539
r_mcbond_other2.529
r_angle_refined_deg1.552
r_angle_other_deg1.005
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.008
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 Atoms2551
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling