2XS3 | pdb_00002xs3

Structure of karilysin catalytic MMP domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MNCPDB ENTRY 1MNC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293CRYSTALLIZATION ASSAYS WERE PERFORMED BY THE SITTING-DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTIONS WERE PREPARED BY A TECAN ROBOT AND CRYSTALLIZATION DROPS WERE DISPENSED ON 96X2-WELL MRC PLATES (INNOVADYNE) BY A CARTESIAN (GENOMIC SOLUTIONS) NANODROP ROBOT AT THE HIGH-THROUGHPUT CRYSTALLOGRAPHY PLATFORM AT BARCELONA SCIENCE PARK. CRYSTALS SUITABLE FOR STRUCTURE ANALYSIS WERE OBTAINED FOR UNBOUND KLY18 IN A BRUKER STEADY-TEMPERATURE CRYSTAL FARM AT 20C FROM DROPS CONTAINING 100NL OF PROTEIN SOLUTION (AT 9MG ML-1 IN 5MM TRIS-HCL, PH8.0, 0.02% SODIUM AZIDE) AND 100NL OF 45% 2-METHYL-2,4-PENTANEDIOL, 0.2M AMMONIUM ACETATE, 0.1M TRIS-HCL, PH8.5 AS RESERVOIR SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
2.5451.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.37α = 90
b = 53.11β = 134.55
c = 86.3γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.445.399.30.0914.84.11541138.4
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)
12.42.5395.90.512.53.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1MNC2.4501470370899.280.191970.188770.20.258720.26RANDOM33.731
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]
3.22.49-1.71.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.332
r_dihedral_angle_3_deg17.064
r_dihedral_angle_4_deg15.179
r_dihedral_angle_1_deg6.729
r_scangle_it2.264
r_scbond_it1.46
r_angle_refined_deg1.321
r_mcangle_it1.109
r_angle_other_deg0.886
r_mcbond_it0.603
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2702
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing