X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5IOL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Protein-ligand: 465 micro-M hMMP12 F171D E219Q, 0.020 M acetohydroxamic acid, 10% DMSO, 0.5 milli-M inhibitor (DC28). Precipitant: 40.5% PEG4K, 10% dioxane, 2% ethylene glycol, 0.18 M imidazole piperidine, pH 8.5. Cryoprotectant:40% cryomix CM12: (,25 % diethylene glycol + 12.5 % glycerol + 25 % 1,2-propanediol + 12.5 % 1,4-dioxane), 25% PEG 6K, 0.1 M TRIS HCl, pH 8.0.
Crystal Properties
Matthews coefficientSolvent content
2.2244.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.98α = 90
b = 63.51β = 102.31
c = 78.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2014-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.9801SOLEILPROXIMA 2

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
11.9544.5698.40.230.214.794.4945133-324.46
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)
11.95286.80.9851.684.25

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 REPLACEMENTTHROUGHOUT5IOL2.0532.8736421191798.60.2120.210.249RANDOM30
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]
-0.180.16-0.240.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.186
r_dihedral_angle_4_deg21.241
r_dihedral_angle_3_deg15.284
r_long_range_B_refined8.274
r_dihedral_angle_1_deg6.89
r_mcangle_it4.344
r_scbond_it3.833
r_mcbond_it3.05
r_angle_refined_deg1.938
r_chiral_restr0.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.186
r_dihedral_angle_4_deg21.241
r_dihedral_angle_3_deg15.284
r_long_range_B_refined8.274
r_dihedral_angle_1_deg6.89
r_mcangle_it4.344
r_scbond_it3.833
r_mcbond_it3.05
r_angle_refined_deg1.938
r_chiral_restr0.159
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5080
Nucleic Acid Atoms
Solvent Atoms466
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building