6YYR

Structure of Cathepsin S in complex with Compound 20b


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82770.10 M sodium citrate pH 4.8, 0.2 M ammonium sulfate, 29% w/v PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.7955.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.84α = 90
b = 85.84β = 90
c = 151.9γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

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
11.33093.60.0630.0220.99916.68129490
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)
11.31.3796.40.7070.2560.7482.87.3

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 structure1.329.779129488648492.890.0980.09660.130615.978
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]
0.0060.006-0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.365
r_dihedral_angle_4_deg16.031
r_dihedral_angle_1_deg14.145
r_dihedral_angle_3_deg11.846
r_dihedral_angle_other_3_deg10.551
r_lrange_it4.882
r_lrange_other4.063
r_rigid_bond_restr3.999
r_scbond_it3.317
r_scbond_other3.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.365
r_dihedral_angle_4_deg16.031
r_dihedral_angle_1_deg14.145
r_dihedral_angle_3_deg11.846
r_dihedral_angle_other_3_deg10.551
r_lrange_it4.882
r_lrange_other4.063
r_rigid_bond_restr3.999
r_scbond_it3.317
r_scbond_other3.317
r_scangle_it3.288
r_scangle_other3.288
r_angle_refined_deg2.18
r_mcangle_it1.706
r_mcangle_other1.706
r_angle_other_deg1.646
r_mcbond_it1.419
r_mcbond_other1.418
r_symmetry_nbd_refined0.268
r_nbd_other0.263
r_chiral_restr0.252
r_nbd_refined0.224
r_symmetry_xyhbond_nbd_refined0.221
r_xyhbond_nbd_refined0.2
r_symmetry_nbd_other0.192
r_nbtor_refined0.185
r_symmetry_nbtor_other0.093
r_symmetry_xyhbond_nbd_other0.076
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3428
Nucleic Acid Atoms
Solvent Atoms878
Heterogen Atoms135

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing