2J83

Ulilysin metalloprotease in complex with batimastat.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5VAPOUR-DIFFUSION CRYSTALLISATION METHOD FROM SITTING DROPS CONSISTING OF 1 MICROLITER OF PROULILYSIN (5 MG/ML IN 30MM TRIS-HCL PH 7.5, 2MM DITHIOTHREITOL, 100MM NACL), 1 MICROLITER OF RESERVOIR SOLUTION (18% PEG 8000, 0.1M 2-MORPHOLINOETHANESULFONIC ACID, PH6.5, 0.2M CACL2) AND, OPTIONALLY, 0.2 MICROLITER OF 0.1M SPERMIDINE OR 30% 2, 4-METHYLPENTANEDIOL AS ADDITIVES.
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.85α = 90
b = 60.73β = 90
c = 168.94γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
1245.6970.0424.23.815461616
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)
122.1190.30.0713.93.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2CKI2503960652096.40.1610.1610.211RANDOM17
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]
-1.253.05-1.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.003
r_dihedral_angle_4_deg14.841
r_dihedral_angle_3_deg12.978
r_dihedral_angle_1_deg5.969
r_scangle_it1.927
r_scbond_it1.204
r_angle_refined_deg1.181
r_mcangle_it0.68
r_mcbond_it0.384
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.003
r_dihedral_angle_4_deg14.841
r_dihedral_angle_3_deg12.978
r_dihedral_angle_1_deg5.969
r_scangle_it1.927
r_scbond_it1.204
r_angle_refined_deg1.181
r_mcangle_it0.68
r_mcbond_it0.384
r_nbtor_refined0.301
r_nbd_refined0.183
r_symmetry_hbond_refined0.172
r_symmetry_vdw_refined0.147
r_xyhbond_nbd_refined0.112
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4038
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling