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Complement factor B protease domain in complex with the reversible inhibitor ((2S,4S)-1-((5,7-dimethyl-1H-indol-4-yl)methyl)-4-methoxypiperidin-2-yl)methanol.
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 2.5 M ammonium sulfate, 0.1 mM sodium acetate (pH 4.6), 2 mM inhibitor
Crystal Properties Matthews coefficient Solvent content 2.52 51.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.592 α = 90 b = 98.06 β = 99.174 c = 61.721 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 2011-06-01 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) 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 1.77 51.754 99.5 0.052 16.56 3.4 63253 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.83 99.9 0.33 4.25 3.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1DLE 1.77 51.754 63252 3163 99.511 0.191 0.1894 0.1892 0.2198 0.2193 24.277
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] -0.051 -0.085 0.095 -0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.041 r_dihedral_angle_4_deg 16.456 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_1_deg 6.79 r_lrange_it 5.799 r_lrange_other 5.775 r_scangle_it 4.826 r_scangle_other 4.78 r_scbond_it 3.2 r_scbond_other 3.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.041 r_dihedral_angle_4_deg 16.456 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_1_deg 6.79 r_lrange_it 5.799 r_lrange_other 5.775 r_scangle_it 4.826 r_scangle_other 4.78 r_scbond_it 3.2 r_scbond_other 3.143 r_mcangle_other 2.789 r_mcangle_it 2.788 r_mcbond_it 2.015 r_mcbond_other 2.012 r_angle_refined_deg 1.599 r_angle_other_deg 1.36 r_nbd_refined 0.192 r_symmetry_nbd_refined 0.19 r_nbd_other 0.186 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.102 r_ncsr_local_group_1 0.093 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.079 r_symmetry_metal_ion_refined 0.048 r_metal_ion_refined 0.033 r_bond_refined_d 0.011 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 4463 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing