6IC6

Human cathepsin-C in complex with cyclopropyl peptidyl nitrile inhibitor 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin-house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529120.0 % (w/v) PEG 6000 0.1 M sodium citrate pH 5.0
Crystal Properties
Matthews coefficientSolvent content
2.7955.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.69α = 90
b = 87.77β = 90
c = 115.03γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.03796MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.89828.02697.20.0518.43.734042
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.8981.95960.3943.4

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 SYNTHESISTHROUGHOUTin-house structure1.89828.02634042168497.180.1490.1470.185827.472
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]
0.391.623-2.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.483
r_dihedral_angle_4_deg23.378
r_dihedral_angle_3_deg13.309
r_dihedral_angle_1_deg9.377
r_lrange_it5.593
r_lrange_other5.593
r_scangle_it2.735
r_scangle_other2.735
r_mcangle_it2.474
r_mcangle_other2.474
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.483
r_dihedral_angle_4_deg23.378
r_dihedral_angle_3_deg13.309
r_dihedral_angle_1_deg9.377
r_lrange_it5.593
r_lrange_other5.593
r_scangle_it2.735
r_scangle_other2.735
r_mcangle_it2.474
r_mcangle_other2.474
r_angle_refined_deg1.843
r_scbond_it1.728
r_scbond_other1.728
r_mcbond_it1.581
r_mcbond_other1.581
r_angle_other_deg1.451
r_symmetry_nbd_refined0.299
r_nbd_other0.243
r_nbd_refined0.212
r_symmetry_xyhbond_nbd_refined0.197
r_xyhbond_nbd_refined0.194
r_nbtor_refined0.184
r_symmetry_nbd_other0.182
r_symmetry_xyhbond_nbd_other0.132
r_chiral_restr0.092
r_symmetry_nbtor_other0.083
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2760
Nucleic Acid Atoms
Solvent Atoms296
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing