X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OY2PDB ENTRY 2OY2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293MMP-8 at 400 micro-M co-crystallization with peptidic inhibitor with reservoir solution 17.5% PEG 20K, 0.1 M MES, 0.125 M NACL. VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K. Inhibitor exchange: 24hr soak in 25% PEG 4K instead of 17.5% PEG20K with 100 micro-M E1S inhibitor in 6 micro-L volume cryoprotectant is 12% PEG10K, 13.75% MPEG2K, 5% di-ethylene glycol, 10% 1,2-propanediol, 10% glycerol, 0.025 M MES PH 5.5, 30 sec cryoprotectant soak
Crystal Properties
Matthews coefficientSolvent content
2.2545.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.719α = 90
b = 69.369β = 90
c = 70.312γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rbent cylindrical mirror2011-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97242ESRFID23-1

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
11.886098.10.2470.2228.95.261365013397-324.39
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.882.0199.61.0260.9192.085.212439

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2OY21.8834.69129701272966798.140.194090.190870.2578RANDOM21.835
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]
-1.73-1.793.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.691
r_dihedral_angle_4_deg21.05
r_dihedral_angle_3_deg16.025
r_dihedral_angle_1_deg7.547
r_scangle_it4.249
r_scbond_it3.103
r_mcangle_it2.071
r_angle_refined_deg2.012
r_mcbond_it1.278
r_chiral_restr0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.691
r_dihedral_angle_4_deg21.05
r_dihedral_angle_3_deg16.025
r_dihedral_angle_1_deg7.547
r_scangle_it4.249
r_scbond_it3.103
r_mcangle_it2.071
r_angle_refined_deg2.012
r_mcbond_it1.278
r_chiral_restr0.24
r_bond_refined_d0.022
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1253
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms42

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling