6YYP

Structure of Cathepsin S in complex with Compound 2


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.828554% v/v tacsimate pH 6.8
Crystal Properties
Matthews coefficientSolvent content
2.7755.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.689α = 90
b = 118.689β = 90
c = 205.586γ = 120
Symmetry
Space GroupH 3 2

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
12.053098.70.1350.0660.997.43.934644
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)
12.052.1699.40.6630.320.6322.54

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 structure2.0529.69134643170898.0890.1440.14150.187731.859
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]
0.3010.150.301-0.975
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.111
r_dihedral_angle_4_deg17.752
r_dihedral_angle_3_deg14.491
r_dihedral_angle_1_deg6.793
r_lrange_it6.682
r_lrange_other6.588
r_scangle_it3.603
r_scangle_other3.602
r_scbond_it2.288
r_scbond_other2.287
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.111
r_dihedral_angle_4_deg17.752
r_dihedral_angle_3_deg14.491
r_dihedral_angle_1_deg6.793
r_lrange_it6.682
r_lrange_other6.588
r_scangle_it3.603
r_scangle_other3.602
r_scbond_it2.288
r_scbond_other2.287
r_mcangle_it1.997
r_mcangle_other1.996
r_angle_refined_deg1.73
r_angle_other_deg1.453
r_mcbond_it1.327
r_mcbond_other1.302
r_symmetry_xyhbond_nbd_refined0.379
r_symmetry_nbd_refined0.248
r_nbd_other0.217
r_nbd_refined0.211
r_xyhbond_nbd_refined0.193
r_symmetry_nbd_other0.18
r_nbtor_refined0.177
r_chiral_restr0.087
r_symmetry_nbtor_other0.082
r_symmetry_xyhbond_nbd_other0.08
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3448
Nucleic Acid Atoms
Solvent Atoms444
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing