6YYQ

Structure of Cathepsin S in complex with Compound 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherunpublished isomorphous structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.32850.2 M potassium formate pH 7.3, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2645.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.765α = 90
b = 92.765β = 90
c = 182.893γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.5128.8299.80.0960.0370.99811.96.531846
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.512.6599.90.6230.2320.9132.66.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUEunpublished isomorphous structure2.5128.8231800159999.7430.2130.20980.280274.379
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]
1.7760.8881.776-5.762
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.737
r_dihedral_angle_3_deg18.151
r_dihedral_angle_4_deg14.41
r_dihedral_angle_1_deg7.031
r_lrange_it6.523
r_lrange_other6.513
r_mcangle_other3.321
r_mcangle_it3.32
r_scangle_it3.274
r_scangle_other3.274
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.737
r_dihedral_angle_3_deg18.151
r_dihedral_angle_4_deg14.41
r_dihedral_angle_1_deg7.031
r_lrange_it6.523
r_lrange_other6.513
r_mcangle_other3.321
r_mcangle_it3.32
r_scangle_it3.274
r_scangle_other3.274
r_mcbond_it2.109
r_mcbond_other2.105
r_scbond_it1.999
r_scbond_other1.999
r_angle_refined_deg1.546
r_angle_other_deg1.286
r_symmetry_nbd_refined0.288
r_symmetry_xyhbond_nbd_refined0.254
r_nbd_other0.245
r_xyhbond_nbd_refined0.21
r_nbd_refined0.206
r_symmetry_nbd_other0.188
r_nbtor_refined0.171
r_symmetry_xyhbond_nbd_other0.11
r_ncsr_local_group_60.104
r_ncsr_local_group_50.103
r_ncsr_local_group_30.099
r_symmetry_nbtor_other0.079
r_chiral_restr0.076
r_ncsr_local_group_20.07
r_ncsr_local_group_10.069
r_ncsr_local_group_40.064
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6892
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing