5L7F

Crystal structure of MMP12 mutant K421A in complex with RXP470.1 conjugated with fluorophore Cy5,5 in space group P21.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CZM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.5293protein: MMP12-F171D-K241A 661 micro-M + 10 milli-M AHA, 10% DMSO, 0.5 milli-M fluorescent inhibitor (R47-CY5) precipitant: 20% PEG4K, 2% gamma valerolactone, 0.2 milli-M TRIS pH 9.5 40% CM26 ((12.5 % diethylene glycol + 12.5 % ethylene glycol + 12.5 % glycerol + 25 % 2,3-butanediol + 12.5 % DMSO), 25% MPEG 6K
Crystal Properties
Matthews coefficientSolvent content
2.4850.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.92α = 90
b = 70.37β = 104.61
c = 52.22γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirrors2015-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.978570SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)CC (Half)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
11.7947.3496.90.1450.1130.9886.872.38686060363601-3
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)
11.791.8498.40.9471.432.36172043

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 REPLACEMENTTHROUGHOUT5CZM1.847.3430250159399.330.176560.17560.19464RANDOM21.924
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]
1.01-1.96-1.521.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.784
r_dihedral_angle_4_deg18.917
r_dihedral_angle_3_deg12.698
r_long_range_B_refined8.466
r_long_range_B_other8.214
r_dihedral_angle_1_deg6.42
r_scangle_other5.036
r_scbond_it3.823
r_scbond_other3.821
r_mcangle_it3.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.784
r_dihedral_angle_4_deg18.917
r_dihedral_angle_3_deg12.698
r_long_range_B_refined8.466
r_long_range_B_other8.214
r_dihedral_angle_1_deg6.42
r_scangle_other5.036
r_scbond_it3.823
r_scbond_other3.821
r_mcangle_it3.015
r_mcangle_other3.014
r_angle_other_deg2.529
r_mcbond_it2.091
r_mcbond_other2.085
r_angle_refined_deg1.8
r_chiral_restr0.111
r_gen_planes_other0.024
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.009
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2468
Nucleic Acid Atoms
Solvent Atoms364
Heterogen Atoms283

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building