X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I2Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Protein-ligand: hMMP12 F67D E219Q 465 micro-M, 0.02M acetohydroxamic acid 0.5 milli-M inhibitor (DC31) 10% DMSO. Precipitant: 32.4% PEG 4K, 8% dioxane, 0.2M imidazole piperidine, pH 8.5. Cryoprotectant: 40% cryomix:(12.5 % diethylene glycol + 12.5 % glycerol + 12.5 % 1,2-propanediol + 25 % DMSO + 25 % 1,4-dioxane) 12% PEG 4K, 10% Dioxane, 0.1 M imidazole piperidine pH 8.5.
Crystal Properties
Matthews coefficientSolvent content
2.1943.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.72α = 90
b = 63.14β = 103.09
c = 78.92γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirrors2015-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.97857SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)CC (Half)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
12.1748.7999.30.10.0960.9979.444.3432560-333.956
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)
12.172.2398.90.5233.063.73

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 REPLACEMENTTHROUGHOUT5I2Z2.1748.7930719161799.360.20850.206150.25324RANDOM36.572
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]
-1.530.98-3.84.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.216
r_dihedral_angle_4_deg17.818
r_dihedral_angle_3_deg12.398
r_long_range_B_refined8.183
r_long_range_B_other8.023
r_dihedral_angle_1_deg6.907
r_scangle_other5.652
r_mcangle_other4.229
r_mcangle_it4.228
r_scbond_it3.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.216
r_dihedral_angle_4_deg17.818
r_dihedral_angle_3_deg12.398
r_long_range_B_refined8.183
r_long_range_B_other8.023
r_dihedral_angle_1_deg6.907
r_scangle_other5.652
r_mcangle_other4.229
r_mcangle_it4.228
r_scbond_it3.68
r_scbond_other3.679
r_mcbond_it2.939
r_mcbond_other2.938
r_angle_refined_deg1.904
r_angle_other_deg1.054
r_chiral_restr0.116
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.004
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4936
Nucleic Acid Atoms
Solvent Atoms430
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
Cootmodel building