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MMP12 in a complex with the dimeric adduct: 5-(5-phenylhydantoin)-5-phenylhydantoin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other internal model: V108-L261 no metal ions.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 50mM imidazole pH 7.5, 200-400mM CaCl, 20% PEG 1k, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.87 34.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.746 α = 90 b = 60.625 β = 103.1 c = 58.403 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2008-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.072250 ESRF ID23-1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.3 41.487 98.2 0.08 0.08 6.9 2.8 65111 65111
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) Redundancy Number Unique Reflections (All) 1 1.3 1.37 89.1 0.635 0.635 1.2 2.1 8579
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT internal model: V108-L261 no metal ions. 1.3 41.487 64982 3294 100 0.1324 0.1302 0.1344 0.1736 0.178 RANDOM 19.7329
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] -0.93 -0.22 0.93 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.981 r_dihedral_angle_4_deg 16.419 r_dihedral_angle_3_deg 10.438 r_dihedral_angle_1_deg 5.567 r_scangle_it 3.724 r_scbond_it 2.695 r_mcangle_it 2.055 r_angle_refined_deg 1.465 r_rigid_bond_restr 1.301 r_mcbond_it 1.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.981 r_dihedral_angle_4_deg 16.419 r_dihedral_angle_3_deg 10.438 r_dihedral_angle_1_deg 5.567 r_scangle_it 3.724 r_scbond_it 2.695 r_mcangle_it 2.055 r_angle_refined_deg 1.465 r_rigid_bond_restr 1.301 r_mcbond_it 1.299 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2451 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 78
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection