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Complement factor D in complex with the inhibitor (S)-pyrrolidine-1,2-dicarboxylic acid 1-[(1-carbamoyl-1H-indol-3-yl)-amide] 2-[(3-trifluoromethoxy-phenyl)-amide]
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other 1HFLF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 MM NACL, 0.5MM NVP-BVT244-NX-1
+ 1 UL RESERVOIR SOLUTION
Crystal Properties Matthews coefficient Solvent content 1.98 37.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.802 α = 90 b = 44.516 β = 117.69 c = 63.744 γ = 90
Symmetry Space Group C 1 2 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 2008-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0001 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 1.37 56.44 98.3 0.085 9.9 3.49 40131 -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 1.37 1.42 90 0.392 2.93 2.56
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 1HFLF 1.55 35.58 26638 1402 99.4 0.15891 0.15515 0.1665 0.23101 0.2353 RANDOM 13.961
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] 0.03 0.04 -0.16 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.068 r_sphericity_free 24.321 r_dihedral_angle_4_deg 22.374 r_dihedral_angle_3_deg 14.978 r_sphericity_bonded 9.467 r_dihedral_angle_1_deg 7.046 r_long_range_B_refined 4.541 r_long_range_B_other 4.54 r_scangle_other 4.455 r_scbond_it 4.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.068 r_sphericity_free 24.321 r_dihedral_angle_4_deg 22.374 r_dihedral_angle_3_deg 14.978 r_sphericity_bonded 9.467 r_dihedral_angle_1_deg 7.046 r_long_range_B_refined 4.541 r_long_range_B_other 4.54 r_scangle_other 4.455 r_scbond_it 4.076 r_scbond_other 4.073 r_rigid_bond_restr 3.901 r_mcangle_other 3.159 r_mcangle_it 3.097 r_mcbond_it 2.82 r_mcbond_other 2.587 r_angle_refined_deg 2.457 r_angle_other_deg 1.265 r_chiral_restr 0.333 r_bond_refined_d 0.03 r_gen_planes_refined 0.016 r_gen_planes_other 0.003 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 1621 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing