6YYN

Structure of Cathepsin S in complex with Compound 14


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82850.1 M sodium citrate pH 4.8, 0.2 M ammonium sulfate, 17% w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.7655.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.671α = 90
b = 85.671β = 90
c = 150.922γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2014-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
12.2219.5199.40.1180.0580.99410.13.928281
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)
12.222.3499.80.680.3440.7322.53.8

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 structure2.2219.5128263143699.0050.1610.15810.21733.279
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]
0.1710.171-0.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.126
r_dihedral_angle_4_deg16.093
r_dihedral_angle_3_deg14.208
r_dihedral_angle_1_deg6.998
r_lrange_it6.963
r_lrange_other6.868
r_scangle_it2.99
r_scangle_other2.99
r_mcangle_it2.137
r_mcangle_other2.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.126
r_dihedral_angle_4_deg16.093
r_dihedral_angle_3_deg14.208
r_dihedral_angle_1_deg6.998
r_lrange_it6.963
r_lrange_other6.868
r_scangle_it2.99
r_scangle_other2.99
r_mcangle_it2.137
r_mcangle_other2.137
r_scbond_other2.037
r_scbond_it2.034
r_angle_refined_deg1.741
r_angle_other_deg1.624
r_mcbond_it1.319
r_mcbond_other1.319
r_nbd_other0.257
r_symmetry_nbd_refined0.217
r_xyhbond_nbd_refined0.203
r_symmetry_xyhbond_nbd_refined0.201
r_nbd_refined0.195
r_symmetry_nbd_other0.188
r_nbtor_refined0.178
r_ncsr_local_group_10.104
r_chiral_restr0.1
r_symmetry_nbtor_other0.082
r_symmetry_xyhbond_nbd_other0.015
r_bond_refined_d0.013
r_bond_other_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3447
Nucleic Acid Atoms
Solvent Atoms478
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing