5N5J | pdb_00005n5j

Human MMP12 in complex with 3-(5-(1,2-dithiolan-3-yl)pentanamido)propane-1-sulfonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y93 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1 M Tris-HCl, 20% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.1642.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.926α = 90
b = 60.47β = 114.55
c = 53.844γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDOXFORD ONYX CCD2015-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.824.4993.40.0760.0315.66.2129168.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8477.40.1750.1753.11.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1Y931.824.291225566093.340.129090.125450.140.195330.2RANDOM15.609
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]
-0.48-0.020.040.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.341
r_sphericity_free19.178
r_dihedral_angle_3_deg11.105
r_sphericity_bonded10.549
r_rigid_bond_restr8.034
r_dihedral_angle_1_deg6.584
r_dihedral_angle_4_deg6.014
r_scangle_other4.71
r_scbond_it4.296
r_scbond_other3.994
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.341
r_sphericity_free19.178
r_dihedral_angle_3_deg11.105
r_sphericity_bonded10.549
r_rigid_bond_restr8.034
r_dihedral_angle_1_deg6.584
r_dihedral_angle_4_deg6.014
r_scangle_other4.71
r_scbond_it4.296
r_scbond_other3.994
r_long_range_B_refined3.919
r_long_range_B_other3.852
r_mcangle_other2.48
r_mcangle_it2.468
r_mcbond_it2.303
r_mcbond_other2.284
r_angle_refined_deg1.979
r_angle_other_deg1.148
r_chiral_restr0.13
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_bond_other_d0.003
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 Atoms1238
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing