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Complement factor B protease domain in complex with the reversible inhibitor 4-((2S,4S)-4-ethoxy-1-((5-methoxy-7-methyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 24 % (w/v) PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris (pH 5.5), 2mM inhibitor
Crystal Properties Matthews coefficient Solvent content 2.54 51.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.463 α = 90 b = 97.446 β = 100.475 c = 61.815 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 2M 2015-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.7 48.723 98.8 0.068 0.081 10.82 3.3 68802 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.77 96.6 0.814 0.991 1.8 3.15
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1dle 1.7 48.723 68598 3435 98.491 0.197 0.1952 0.2267 0.2273 31.753
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] 2.501 4.074 -0.945 -2.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.263 r_dihedral_angle_3_deg 16.208 r_dihedral_angle_4_deg 15.273 r_lrange_it 6.934 r_lrange_other 6.845 r_dihedral_angle_1_deg 6.826 r_scangle_it 5.27 r_scangle_other 5.119 r_mcangle_it 3.715 r_mcangle_other 3.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.263 r_dihedral_angle_3_deg 16.208 r_dihedral_angle_4_deg 15.273 r_lrange_it 6.934 r_lrange_other 6.845 r_dihedral_angle_1_deg 6.826 r_scangle_it 5.27 r_scangle_other 5.119 r_mcangle_it 3.715 r_mcangle_other 3.715 r_scbond_it 3.495 r_scbond_other 3.393 r_mcbond_it 2.544 r_mcbond_other 2.543 r_angle_refined_deg 1.557 r_angle_other_deg 1.322 r_symmetry_xyhbond_nbd_refined 0.231 r_nbd_refined 0.191 r_nbd_other 0.188 r_symmetry_nbd_other 0.186 r_symmetry_nbd_refined 0.184 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.145 r_ncsr_local_group_1 0.096 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.076 r_symmetry_metal_ion_refined 0.069 r_xyhbond_nbd_other 0.063 r_metal_ion_refined 0.037 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4409 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing