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Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DSU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% PEG MME 2000, 0.1M sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 1.99 38.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.151 α = 83.69 b = 66.613 β = 64.36 c = 76.377 γ = 74.65
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 2013-01-01 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) CC (Half) 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 1.54 57.9 84.5 0.072 0.102 0.996 5.82 1.73 142642 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.63 77.2 0.837 1.18 0.381 0.7 1.59
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 1dsu 2 49.23 63676 3351 87.51 0.2216 0.2198 0.2555 0.2608 RANDOM 21.421
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] -0.01 -0.13 0.04 0.14 0.05 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.69 r_dihedral_angle_4_deg 17.992 r_dihedral_angle_3_deg 14.914 r_mcangle_it 4.126 r_mcbond_it 3.31 r_dihedral_angle_1_deg 3.233 r_mcbond_other 3.231 r_angle_other_deg 2.484 r_angle_refined_deg 1.904 r_chiral_restr 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.69 r_dihedral_angle_4_deg 17.992 r_dihedral_angle_3_deg 14.914 r_mcangle_it 4.126 r_mcbond_it 3.31 r_dihedral_angle_1_deg 3.233 r_mcbond_other 3.231 r_angle_other_deg 2.484 r_angle_refined_deg 1.904 r_chiral_restr 0.147 r_bond_other_d 0.035 r_bond_refined_d 0.016 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10266 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing BUSTER refinement