3KEC

Crystal Structure of Human MMP-13 complexed with a phenyl-2H-tetrazole compound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8277Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2 reservoir: 1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2 drop ratio: 5ul protein + 1 ul reservoir, Vapor diffusion, sitting drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3347.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.209α = 90
b = 72.348β = 90
c = 36.356γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMAR CCD 165 mmcrystal monochromator2001-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.04501000.0670.06713.42.61942919429-1.5-320.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.042.11880.1360.1365.82.61948

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.05501841999685.310.170330.168580.20357RANDOM19.235
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]
0.89-0.21-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.937
r_dihedral_angle_4_deg14.46
r_dihedral_angle_3_deg12.978
r_dihedral_angle_1_deg5.751
r_scangle_it1.542
r_scbond_it1.105
r_angle_refined_deg1.067
r_angle_other_deg0.796
r_mcangle_it0.756
r_mcbond_it0.462
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.937
r_dihedral_angle_4_deg14.46
r_dihedral_angle_3_deg12.978
r_dihedral_angle_1_deg5.751
r_scangle_it1.542
r_scbond_it1.105
r_angle_refined_deg1.067
r_angle_other_deg0.796
r_mcangle_it0.756
r_mcbond_it0.462
r_symmetry_vdw_other0.204
r_nbtor_refined0.195
r_nbd_refined0.192
r_nbd_other0.178
r_xyhbond_nbd_refined0.139
r_symmetry_vdw_refined0.139
r_symmetry_hbond_refined0.139
r_metal_ion_refined0.113
r_nbtor_other0.082
r_mcbond_other0.081
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2653
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms96

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing