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Structure determination of a potent, selective antibody inhibitor of human MMP9 (GS-5745 bound to MMP-9)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L6J 1L6J (MMP9), 1F8T (GS-5745 Fab) experimental model PDB 1F8T 1L6J (MMP9), 1F8T (GS-5745 Fab)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Drop:
8% (w/v) PEG 8000
0.1 M HEPES, pH 7.5
50% (v/v) Silver Bullet 21 (Hampton Research)
Reservoir:
22.5% (w/v) PEG 8000
0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.73 67.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.167 α = 90 b = 168.167 β = 90 c = 234.735 γ = 90
Symmetry Space Group P 43 21 2
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 315 2013-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.979 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3 50 100 0.098 8.9 6.1 67959 38.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.09 100 0.465 6.2 5556
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1L6J (MMP9), 1F8T (GS-5745 Fab) 2.999 46.641 1.34 67775 1999 99.81 0.2193 0.2182 0.219 0.257 0.253 42.7273
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 Key Refinement Restraint Deviation f_dihedral_angle_d 13.527 f_angle_d 1.068 f_chiral_restr 0.061 f_bond_d 0.013 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13367 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing