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Catalytic fragment of MASP-2 in complex with its specific inhibitor developed by directed evolution on SGCI scaffold
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q3X domains of PDB entry 1Q3X, and PDB entry 1GL1 experimental model PDB 1GL1 domains of PDB entry 1Q3X, and PDB entry 1GL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 24.5% PEG 5000 MME, 0.164 M ammonium sulphate, 82 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.916 α = 90 b = 62.471 β = 90 c = 114.189 γ = 90
Symmetry Space Group P 21 21 21
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 210 2011-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
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 1.28 40 95.8 0.065 15.1 5.44 90627 90627 -3 16.911
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 1.28 1.3 93.3 0.752 2.54 5.06 3960
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 domains of PDB entry 1Q3X, and PDB entry 1GL1 1.28 38 85991 85991 4584 95.87 0.15875 0.15875 0.15623 0.165 0.20532 0.2109 RANDOM 14.05
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] -0.02 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.955 r_dihedral_angle_4_deg 20.764 r_dihedral_angle_3_deg 13.636 r_scangle_it 8.578 r_dihedral_angle_1_deg 7.099 r_scbond_it 6.428 r_mcangle_it 4.455 r_mcbond_it 3.342 r_rigid_bond_restr 2.938 r_angle_refined_deg 2.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.955 r_dihedral_angle_4_deg 20.764 r_dihedral_angle_3_deg 13.636 r_scangle_it 8.578 r_dihedral_angle_1_deg 7.099 r_scbond_it 6.428 r_mcangle_it 4.455 r_mcbond_it 3.342 r_rigid_bond_restr 2.938 r_angle_refined_deg 2.059 r_mcbond_other 1.363 r_angle_other_deg 1.142 r_chiral_restr 0.134 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2753 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 5
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling