5N7N

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52911:1 PROTEIN (10 MG/ML IN 2 MM BIS- TRIS, PH 6.5, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.085 M TRIS-HCL, PH 8.0, 1.7 M AMMONIUM SULFATE, 1 MM DTT), CRYOCOOLED IN MOTHER LIQUOR, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Crystal Properties
Matthews coefficientSolvent content
2.9558.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.322α = 90
b = 94.981β = 99.28
c = 106.17γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-11.07161ESRFID14-1

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
12.345.8799.70.06914.814.182782-3
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)
12.32.4499.30.4792.79

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 SYNTHESISTHROUGHOUT2.345.8778636414599.730.222180.220170.25999RANDOM40.185
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]
-0.16-0.040.130.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.824
r_dihedral_angle_4_deg19.141
r_dihedral_angle_3_deg15.359
r_dihedral_angle_1_deg7.288
r_long_range_B_refined5.45
r_long_range_B_other5.45
r_scangle_other3.609
r_mcangle_it3.386
r_mcangle_other3.386
r_scbond_it2.235
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.824
r_dihedral_angle_4_deg19.141
r_dihedral_angle_3_deg15.359
r_dihedral_angle_1_deg7.288
r_long_range_B_refined5.45
r_long_range_B_other5.45
r_scangle_other3.609
r_mcangle_it3.386
r_mcangle_other3.386
r_scbond_it2.235
r_scbond_other2.227
r_mcbond_it2.096
r_mcbond_other2.096
r_angle_refined_deg1.45
r_angle_other_deg0.97
r_chiral_restr0.087
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms10963
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling