2OXZ

Human MMP-12 in complex with two peptides PQG and IAG


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82980.1 M Tris-HCl, 30% PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.141.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.546α = 90
b = 60.378β = 115.41
c = 54.449γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDKODAKEnhance Ultra2006-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOTHER

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
11.930.1998.10.1370.1374.75.611726117267.69
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)
1.9298.10.3270.3272.331505

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 1Y931.930.19106911069110331000.214060.214060.206940.28767RANDOM9.801
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]
-0.07-0.180.04-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.378
r_dihedral_angle_4_deg20.653
r_dihedral_angle_3_deg15.894
r_dihedral_angle_1_deg6.783
r_sphericity_bonded4.311
r_scangle_it3.923
r_scbond_it2.777
r_angle_refined_deg1.86
r_mcangle_it1.708
r_rigid_bond_restr1.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.378
r_dihedral_angle_4_deg20.653
r_dihedral_angle_3_deg15.894
r_dihedral_angle_1_deg6.783
r_sphericity_bonded4.311
r_scangle_it3.923
r_scbond_it2.777
r_angle_refined_deg1.86
r_mcangle_it1.708
r_rigid_bond_restr1.317
r_mcbond_it1.134
r_symmetry_hbond_refined0.378
r_nbtor_refined0.312
r_nbd_refined0.224
r_symmetry_vdw_refined0.218
r_xyhbond_nbd_refined0.204
r_metal_ion_refined0.187
r_chiral_restr0.12
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1269
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing