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Crystal structure of MMP12 mutant K421A in complex with RXP470.1 conjugated with fluorophore Cy5,5 in space group P21.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 protein: MMP12-F171D-K241A 661 micro-M + 10 milli-M AHA, 10% DMSO, 0.5 milli-M fluorescent inhibitor (R47-CY5)
precipitant: 20% PEG4K, 2% gamma valerolactone, 0.2 milli-M TRIS pH 9.5
40% CM26 ((12.5 % diethylene glycol + 12.5 % ethylene glycol + 12.5 % glycerol + 25 % 2,3-butanediol + 12.5 % DMSO), 25% MPEG 6K
Crystal Properties Matthews coefficient Solvent content 2.48 50.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.92 α = 90 b = 70.37 β = 104.61 c = 52.22 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 PIXEL DECTRIS PILATUS 6M mirrors 2015-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978570 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 1.79 47.34 96.9 0.145 0.113 0.988 6.87 2.386860603 63601 -3
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 1.79 1.84 98.4 0.947 1.43 2.36172043
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 5CZM 1.8 47.34 30250 1593 99.33 0.17656 0.1756 0.1881 0.19464 0.2049 RANDOM 21.924
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] 1.01 -1.96 -1.52 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.784 r_dihedral_angle_4_deg 18.917 r_dihedral_angle_3_deg 12.698 r_long_range_B_refined 8.466 r_long_range_B_other 8.214 r_dihedral_angle_1_deg 6.42 r_scangle_other 5.036 r_scbond_it 3.823 r_scbond_other 3.821 r_mcangle_it 3.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.784 r_dihedral_angle_4_deg 18.917 r_dihedral_angle_3_deg 12.698 r_long_range_B_refined 8.466 r_long_range_B_other 8.214 r_dihedral_angle_1_deg 6.42 r_scangle_other 5.036 r_scbond_it 3.823 r_scbond_other 3.821 r_mcangle_it 3.015 r_mcangle_other 3.014 r_angle_other_deg 2.529 r_mcbond_it 2.091 r_mcbond_other 2.085 r_angle_refined_deg 1.8 r_chiral_restr 0.111 r_gen_planes_other 0.024 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.009 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2468 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 283
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building