5LAB

Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor NNGH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OS9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293Tris, PEG6000, NNGH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.19α = 90
b = 62.56β = 90
c = 37.26γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.2000ELETTRA5.2R

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
11.3446.40798.47.26.236295
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.341.4192.60.3082.34.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1OS91.342033671257598.50.157890.155150.1945RANDOM21.754
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]
-1.5-0.522.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.048
r_sphericity_free26.636
r_dihedral_angle_3_deg13.286
r_sphericity_bonded8.864
r_dihedral_angle_4_deg8.52
r_dihedral_angle_1_deg6.396
r_long_range_B_refined3.85
r_rigid_bond_restr3.31
r_long_range_B_other3.207
r_scangle_other2.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.048
r_sphericity_free26.636
r_dihedral_angle_3_deg13.286
r_sphericity_bonded8.864
r_dihedral_angle_4_deg8.52
r_dihedral_angle_1_deg6.396
r_long_range_B_refined3.85
r_rigid_bond_restr3.31
r_long_range_B_other3.207
r_scangle_other2.303
r_mcangle_it2.025
r_mcangle_other2.024
r_scbond_it2.021
r_scbond_other2.02
r_angle_refined_deg1.803
r_mcbond_it1.758
r_mcbond_other1.721
r_angle_other_deg1.229
r_chiral_restr0.35
r_bond_refined_d0.035
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1246
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing