3DPE

Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I76PDB ENTRY 1I76

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293Hanging droplets were made by mixing 1.5-3.0ml of protein/inhibitor solution with 5ml of PEG solution (10% PEG6000, 0.2M Mes-NaOH, 0.02% NaN3, pH6.0). Droplets were concentrated against a reservoir buffer containing 1.0-2.0M sodium phosphate, 0.02% NaN3, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9436.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.29α = 90
b = 68.95β = 105.41
c = 32.75γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

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
11.62599.20.1035.74.118154181549.1

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1I761.610180601806017800.210.242random
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]
RMS Deviations
KeyRefinement Restraint Deviation
c_angle_deg1.44
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1282
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms41

Software

Software
Software NamePurpose
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling