4QKZ

X-ray structure of the catalytic domain of MMP-8 with the inhibitor ML115


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DPEPDB entry 3DPE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629310 % PEG 6000, 0.2M MES/NAOH, 1M NA PHOSPHATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.91α = 90
b = 68.69β = 90
c = 70.69γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayPIXELPSI PILATUS 6M2013-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.249.2699.170.0910.2454954549512.98
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)
11.21.399.20.4562.5210641

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 3DPE1.249.2645495505699.170.171970.171970.169520.1937RANDOM9.976
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]
0.250.23-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.967
r_sphericity_free22.661
r_dihedral_angle_4_deg18.927
r_dihedral_angle_3_deg11.074
r_sphericity_bonded8.611
r_dihedral_angle_1_deg6.996
r_rigid_bond_restr2.739
r_long_range_B_refined1.976
r_long_range_B_other1.733
r_angle_refined_deg1.522
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.967
r_sphericity_free22.661
r_dihedral_angle_4_deg18.927
r_dihedral_angle_3_deg11.074
r_sphericity_bonded8.611
r_dihedral_angle_1_deg6.996
r_rigid_bond_restr2.739
r_long_range_B_refined1.976
r_long_range_B_other1.733
r_angle_refined_deg1.522
r_scangle_other1.209
r_scbond_it0.959
r_scbond_other0.959
r_angle_other_deg0.881
r_mcangle_it0.839
r_mcangle_other0.838
r_mcbond_it0.808
r_mcbond_other0.801
r_chiral_restr0.135
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms1282
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms41

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling