2HU6

Crystal structure of human MMP-12 in complex with acetohydroxamic acid and a bicyclic inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y93pdb entry 1Y93

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82980.1 M Tris-HCl, 30% PEG 6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1542.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.25α = 90
b = 60.179β = 114.59
c = 53.974γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmFixed exit double crystal Si [111], horizontally focusing2005-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7A0.93920EMBL/DESY, HAMBURGBW7A

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
11.3249.0899.10.0530.0538.63.1346483464810.41
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)
1.321.3995.60.2820.2822.12.94823

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 1Y931.3225.68315033150331441000.162560.162560.160620.18176RANDOM13.577
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]
0.27-0.33-0.11-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.449
r_dihedral_angle_4_deg16.79
r_dihedral_angle_3_deg9.33
r_dihedral_angle_1_deg5.72
r_sphericity_free2.614
r_scangle_it2.348
r_sphericity_bonded1.86
r_scbond_it1.837
r_rigid_bond_restr1.751
r_mcangle_it1.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.449
r_dihedral_angle_4_deg16.79
r_dihedral_angle_3_deg9.33
r_dihedral_angle_1_deg5.72
r_sphericity_free2.614
r_scangle_it2.348
r_sphericity_bonded1.86
r_scbond_it1.837
r_rigid_bond_restr1.751
r_mcangle_it1.115
r_angle_refined_deg1.1
r_mcbond_it0.76
r_nbtor_refined0.308
r_symmetry_vdw_refined0.202
r_nbd_refined0.183
r_symmetry_hbond_refined0.121
r_xyhbond_nbd_refined0.115
r_chiral_restr0.077
r_metal_ion_refined0.074
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1238
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing