2XU3

CATHEPSIN L WITH A NITRILE INHIBITOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HWNPDB ENTRY 3HWN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.20.1 M CITRIC ACID PH 3.5 25 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9336.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.441α = 90
b = 49.394β = 105.13
c = 46.129γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
10.95098.10.088.113.32139614-39.15
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)
10.9196.50.641.253.19

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3HWN0.944.53125923670693.190.142480.141830.15473RANDOM8.362
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]
0.20.190.07-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.097
r_dihedral_angle_4_deg17.323
r_dihedral_angle_3_deg11.067
r_sphericity_free7.963
r_dihedral_angle_1_deg5.914
r_rigid_bond_restr4.626
r_sphericity_bonded2.938
r_angle_refined_deg1.556
r_angle_other_deg0.878
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.097
r_dihedral_angle_4_deg17.323
r_dihedral_angle_3_deg11.067
r_sphericity_free7.963
r_dihedral_angle_1_deg5.914
r_rigid_bond_restr4.626
r_sphericity_bonded2.938
r_angle_refined_deg1.556
r_angle_other_deg0.878
r_chiral_restr0.101
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1697
Nucleic Acid Atoms
Solvent Atoms373
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing