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Complement factor D in complex with the inhibitor (1R,3S,5R)-2-Aza-bicyclo[3.1.0]hexane-2,3-dicarboxylic acid 2-[(1-carbamoyl-1H-indol-3-yl)-amide] 3-[(3-trifluoromethoxy-phenyl)-amide]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BIO 1TACE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 27% PEG 3350
100 mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.862 α = 90 b = 49.444 β = 106.51 c = 39.238 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 CCD MARRESEARCH 2008-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99999 SLS X10SA
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 1.25 53.56 97.7 0.032 17.82 2.88 55553 -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 1.25 1.28 84.5 0.326 2.24 1.88
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TACE 1.25 26.78 52774 2778 97.84 0.13035 0.12789 0.17791 0.1985 RANDOM 18.891
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] 0.14 -0.26 -0.27 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.505 r_sphericity_free 32.416 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_4_deg 14.408 r_sphericity_bonded 13.741 r_dihedral_angle_1_deg 6.744 r_long_range_B_refined 5.813 r_long_range_B_other 5.811 r_rigid_bond_restr 5.628 r_scangle_other 5.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.505 r_sphericity_free 32.416 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_4_deg 14.408 r_sphericity_bonded 13.741 r_dihedral_angle_1_deg 6.744 r_long_range_B_refined 5.813 r_long_range_B_other 5.811 r_rigid_bond_restr 5.628 r_scangle_other 5.114 r_scbond_it 4.555 r_scbond_other 4.553 r_mcangle_other 3.54 r_mcangle_it 3.538 r_mcbond_it 2.994 r_mcbond_other 2.981 r_angle_refined_deg 2.521 r_angle_other_deg 1.497 r_chiral_restr 0.536 r_bond_refined_d 0.029 r_gen_planes_refined 0.015 r_gen_planes_other 0.004 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1700 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing