6EKN

Crystal structure of MMP12 in complex with inhibitor BE7.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I03 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP10293Protein: 1 micro-L MMP12 at 290 micro-M with 10 milli-M acetohydroxamate + 0.1 Micro-L BE6 from 10 milii-M in 100% DMSO Precipitant: 17% PEG 20K, 250 milli-M NaCl, 100 milii-M TRIS HCl, pH 10.0. cryoprotectant: 40% (25 % di-ethylene glycol + 25 % glycerol + 25 % 1,2-propanediol) 10 % PEG 10K, 200 milli-M NaCl, 100 milli-M AAB (Na acetate,N-(2-Acetamido)iminodiacetic acid (ADA), Bicine) 10% acid/90% basic
Crystal Properties
Matthews coefficientSolvent content
2.1643.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.56α = 90
b = 60.35β = 116.1
c = 54.56γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9Mmicrofocus2016-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.980035SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
11.236.7499.30.0880.0960.99810.216.6146976-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2394.71.651.80.320.986.18

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 REPLACEMENTTHROUGHOUT4I031.236.7444626234999.430.145740.14420.17523RANDOM20.711
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]
0.22-0.21-0.050.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.284
r_sphericity_free22.953
r_dihedral_angle_4_deg18.293
r_dihedral_angle_3_deg14.134
r_sphericity_bonded10.025
r_rigid_bond_restr8.512
r_dihedral_angle_1_deg6.259
r_long_range_B_refined5.075
r_long_range_B_other4.875
r_scbond_it4.594
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.284
r_sphericity_free22.953
r_dihedral_angle_4_deg18.293
r_dihedral_angle_3_deg14.134
r_sphericity_bonded10.025
r_rigid_bond_restr8.512
r_dihedral_angle_1_deg6.259
r_long_range_B_refined5.075
r_long_range_B_other4.875
r_scbond_it4.594
r_scbond_other4.594
r_scangle_other4.587
r_mcangle_it3.878
r_mcangle_other3.877
r_mcbond_it2.95
r_mcbond_other2.948
r_angle_refined_deg2.377
r_angle_other_deg1.18
r_chiral_restr0.154
r_bond_refined_d0.027
r_gen_planes_refined0.014
r_bond_other_d0.004
r_gen_planes_other0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1246
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building