3KRY

Crystal structure of MMP-13 in complex with SC-78080


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4277100mM Hepes buffer, pH 7.4 1.4M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2846.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.317α = 92.42
b = 70.016β = 94.23
c = 69.094γ = 104.94
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMirrors2000-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9209546273-314.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.919.6846273242594.970.208790.20630.25571RANDOM14.852
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]
0.12-0.090.29-0.620.210.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.169
r_dihedral_angle_4_deg21.101
r_dihedral_angle_3_deg14.468
r_dihedral_angle_1_deg6.113
r_scangle_it2.006
r_scbond_it1.264
r_angle_refined_deg1.102
r_mcangle_it0.88
r_angle_other_deg0.798
r_mcbond_it0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.169
r_dihedral_angle_4_deg21.101
r_dihedral_angle_3_deg14.468
r_dihedral_angle_1_deg6.113
r_scangle_it2.006
r_scbond_it1.264
r_angle_refined_deg1.102
r_mcangle_it0.88
r_angle_other_deg0.798
r_mcbond_it0.48
r_mcbond_other0.093
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5189
Nucleic Acid Atoms
Solvent Atoms522
Heterogen Atoms156

Software

Software
Software NamePurpose
MAR345data collection
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing