4DPE

Structure of MMP3 complexed with a platinum-based inhibitor.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SLNpdb entry 1SLN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529325-30% PEG 8000, 10 mM CaCl2, 100 mM TRIS , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0239.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.206α = 90
b = 77.714β = 90
c = 105.615γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

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
11.8362.699.90.0392854928549
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.922.05100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1SLN1.9638.862854921209213399.990.184430.184430.179640.2307RANDOM27.873
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]
0.03-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.754
r_dihedral_angle_4_deg23.337
r_dihedral_angle_3_deg17.113
r_dihedral_angle_1_deg6.734
r_scangle_it5.085
r_scbond_it3.354
r_mcangle_it2.259
r_angle_refined_deg1.968
r_mcbond_it1.323
r_chiral_restr0.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.754
r_dihedral_angle_4_deg23.337
r_dihedral_angle_3_deg17.113
r_dihedral_angle_1_deg6.734
r_scangle_it5.085
r_scbond_it3.354
r_mcangle_it2.259
r_angle_refined_deg1.968
r_mcbond_it1.323
r_chiral_restr0.143
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2663
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms39

Software

Software
Software NamePurpose
CrystalCleardata collection
ILMLIONEmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
ILMLIONEphasing