2XS4

Structure of karilysin catalytic MMP domain in complex with magnesium


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1277CRYSTALS OF MAGNESIUM-BOUND KLY18 WERE OBTAINED AT 4C BY MIXING PROTEIN SOLUTION PREINCUBATED WITH CALCIUM (AT 7.3MG ML-1 IN 5MM TRIS-HCL, PH8.0, 5MM CALCIUM CHLORIDE, 0.02% SODIUM AZIDE) AND 14% SODIUM POLYACRYLATE 5100, 20MM MAGNESIUM CHLORIDE, 0.1M HEPES, PH7.5 IN A VOLUME RATIO OF 1:3. THE LATTER CONDITIONS WERE SCALED UP TO THE MICROLITER RANGE WITH 24-WELL CRYSCHEM CRYSTALLIZATION DISHES (HAMPTON RESEARCH).
Crystal Properties
Matthews coefficientSolvent content
2.5752.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.79α = 90
b = 85.79β = 90
c = 53.48γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.730.3990.0337.17.22122518.9
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)
11.71.7995.90.1210.84.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2XS31.7502040382098.860.158780.157760.18575RANDOM16.982
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]
0.180.18-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.114
r_dihedral_angle_4_deg16.538
r_dihedral_angle_3_deg11.698
r_dihedral_angle_1_deg5.292
r_scangle_it1.959
r_scbond_it1.225
r_angle_refined_deg1.034
r_mcangle_it0.873
r_angle_other_deg0.822
r_mcbond_it0.464
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.114
r_dihedral_angle_4_deg16.538
r_dihedral_angle_3_deg11.698
r_dihedral_angle_1_deg5.292
r_scangle_it1.959
r_scbond_it1.225
r_angle_refined_deg1.034
r_mcangle_it0.873
r_angle_other_deg0.822
r_mcbond_it0.464
r_mcbond_other0.084
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms1351
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing