2OXU

Uninhibited form of human MMP-12


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% PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1743.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.545α = 90
b = 60.751β = 115.64
c = 54.264γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHFixed exit double crystal Si [111], horizontally focussing2006-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7AEMBL/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
11.2419.6397.20.0790.0793.85.841969419697.17
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)
1.241.384.80.1260.1265.15.25315

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 1Y931.2419.64381643816438041000.19840.19840.19660.2163RANDOM10.993
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]
-0.16-0.180.09-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.493
r_dihedral_angle_4_deg11.622
r_dihedral_angle_3_deg11.215
r_dihedral_angle_1_deg5.597
r_sphericity_free2.602
r_scangle_it2.141
r_sphericity_bonded2.127
r_scbond_it1.516
r_mcangle_it1.149
r_angle_refined_deg1.031
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.493
r_dihedral_angle_4_deg11.622
r_dihedral_angle_3_deg11.215
r_dihedral_angle_1_deg5.597
r_sphericity_free2.602
r_scangle_it2.141
r_sphericity_bonded2.127
r_scbond_it1.516
r_mcangle_it1.149
r_angle_refined_deg1.031
r_rigid_bond_restr0.85
r_mcbond_it0.745
r_nbtor_refined0.302
r_nbd_refined0.186
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.085
r_symmetry_hbond_refined0.084
r_metal_ion_refined0.08
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.004
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1238
Nucleic Acid Atoms
Solvent Atoms235
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing