5N5K

Human catalytic MMP-12 in complex with 5-(1,2-dithiolan-3-yl)-N-(3-hydroxypropyl)pentanamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y93 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1 M Tris-HCl, 20% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.1542.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.79α = 90
b = 60.17β = 114.61
c = 53.73γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDOXFORD ONYX CCD2016-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA1.54

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
11.825.6394.50.06224.16.81293522.3
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)
11.81.978.30.423.654.2

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 REPLACEMENTTHROUGHOUT1Y931.825.621228264795.140.170170.167210.22736RANDOM16.315
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]
1.14-0.11-0.47-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.953
r_dihedral_angle_4_deg14.032
r_dihedral_angle_3_deg13.199
r_long_range_B_refined7.686
r_long_range_B_other7.467
r_dihedral_angle_1_deg7.036
r_scangle_other3.48
r_scbond_it2.236
r_angle_refined_deg2.16
r_scbond_other2.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.953
r_dihedral_angle_4_deg14.032
r_dihedral_angle_3_deg13.199
r_long_range_B_refined7.686
r_long_range_B_other7.467
r_dihedral_angle_1_deg7.036
r_scangle_other3.48
r_scbond_it2.236
r_angle_refined_deg2.16
r_scbond_other2.099
r_mcangle_other1.885
r_mcangle_it1.879
r_angle_other_deg1.225
r_mcbond_it1.153
r_mcbond_other1.092
r_chiral_restr0.138
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_bond_other_d0.005
r_gen_planes_other0.002
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 Atoms1227
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing