5N7Q

CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICINUS (IRCD1) IN COMPLEX WITH THE INHIBITOR PEPSTATIN A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52911:1 PROTEIN (5 MG/ML IN 2.5 MM SODIUM FORMATE, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.14 M SODIUM CHLORIDE, 0.07 M BIS-TRIS, PH 5.5, 17.5% PEG3350, 1 MM DTT), CRYOCOOLED AFTER A QUICK SOAK IN RESERVOIR BUFFER + 30% PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Crystal Properties
Matthews coefficientSolvent content
2.0740.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.14α = 90
b = 82.82β = 91.13
c = 61.39γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252012-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.45561.378980.080.087.23104842
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)
11.4551.5398.60.2270.2273.1

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 SYNTHESISTHROUGHOUT1.4561.38101593533599.910.146290.145220.16646RANDOM13.814
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]
0.120.02-0.12-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.09
r_dihedral_angle_4_deg18.246
r_dihedral_angle_3_deg11.08
r_dihedral_angle_1_deg8.761
r_long_range_B_refined4.842
r_long_range_B_other4.841
r_scangle_other2.001
r_angle_refined_deg1.5
r_mcangle_other1.381
r_mcangle_it1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.09
r_dihedral_angle_4_deg18.246
r_dihedral_angle_3_deg11.08
r_dihedral_angle_1_deg8.761
r_long_range_B_refined4.842
r_long_range_B_other4.841
r_scangle_other2.001
r_angle_refined_deg1.5
r_mcangle_other1.381
r_mcangle_it1.38
r_scbond_it1.269
r_scbond_other1.269
r_angle_other_deg0.983
r_mcbond_it0.877
r_mcbond_other0.873
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.002
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 Atoms5219
Nucleic Acid Atoms
Solvent Atoms1308
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling