3IOQ

Crystal structure of the Carica candamarcensis cysteine protease CMS1MS2 in complex with E-64.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MEGModel predicted by SwissModel using the primary structure of CMS1MS2 and the structures of caricain (PDBID 1MEG), chymopapain (PDBID 1YAL) and papain (PDBID 1PPN)
experimental modelPDB 1YALModel predicted by SwissModel using the primary structure of CMS1MS2 and the structures of caricain (PDBID 1MEG), chymopapain (PDBID 1YAL) and papain (PDBID 1PPN)
experimental modelPDB 1PPNModel predicted by SwissModel using the primary structure of CMS1MS2 and the structures of caricain (PDBID 1MEG), chymopapain (PDBID 1YAL) and papain (PDBID 1PPN)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52910.2 M ammonium sulfate, 25% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.564.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.639α = 90
b = 73.639β = 90
c = 118.786γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDVertical Collimating Mirror, DCM, Toroidal Focusing Mirror2008-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.458LNLSW01B-MX2

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
11.8762.61000.08145.828.12779227792
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)
1.871.931000.2511727.82270

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTModel predicted by SwissModel using the primary structure of CMS1MS2 and the structures of caricain (PDBID 1MEG), chymopapain (PDBID 1YAL) and papain (PDBID 1PPN)1.8762.6112773927714139599.910.1640.1640.1620.193RANDOM22.258
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]
0.060.06-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.985
r_dihedral_angle_4_deg16.584
r_dihedral_angle_3_deg12.412
r_dihedral_angle_1_deg5.637
r_scangle_it3.659
r_scbond_it2.488
r_mcangle_it1.458
r_angle_refined_deg1.301
r_mcbond_it1.238
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.985
r_dihedral_angle_4_deg16.584
r_dihedral_angle_3_deg12.412
r_dihedral_angle_1_deg5.637
r_scangle_it3.659
r_scbond_it2.488
r_mcangle_it1.458
r_angle_refined_deg1.301
r_mcbond_it1.238
r_nbtor_refined0.307
r_nbd_refined0.222
r_symmetry_hbond_refined0.208
r_symmetry_vdw_refined0.194
r_xyhbond_nbd_refined0.148
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1689
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms110

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
AMoREphasing