3KEJ

Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-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
2.8456.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.883α = 90
b = 96.457β = 90
c = 36.638γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 210crystal monochromator2005-06-12MSINGLE 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
12.2301000.1120.11214.54.82245122451-0.5-127.3
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)
2.22.2896.30.370.374.43.41895

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 SYNTHESISTHROUGHOUT2.329.81864698999.590.186020.18340.23611RANDOM8.15
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]
-0.751.09-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.673
r_dihedral_angle_4_deg25.445
r_dihedral_angle_3_deg13.564
r_dihedral_angle_1_deg5.881
r_scangle_it1.59
r_angle_refined_deg1.153
r_scbond_it1.092
r_angle_other_deg0.804
r_mcangle_it0.734
r_mcbond_it0.428
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.673
r_dihedral_angle_4_deg25.445
r_dihedral_angle_3_deg13.564
r_dihedral_angle_1_deg5.881
r_scangle_it1.59
r_angle_refined_deg1.153
r_scbond_it1.092
r_angle_other_deg0.804
r_mcangle_it0.734
r_mcbond_it0.428
r_nbtor_refined0.195
r_symmetry_vdw_other0.193
r_symmetry_hbond_refined0.189
r_nbd_refined0.183
r_nbd_other0.181
r_xyhbond_nbd_refined0.15
r_symmetry_vdw_refined0.141
r_metal_ion_refined0.11
r_nbtor_other0.086
r_mcbond_other0.08
r_chiral_restr0.067
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2531
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms74

Software

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