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Complement factor D in complex with the inhibitor 2-(2-(3'-(aminomethyl)-[1,1'-biphenyl]-3-carboxamido)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 5.5 293 25% PEGME 3350, 100 mM Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 1.71 28.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.964 α = 83.03 b = 39.235 β = 75.34 c = 63.502 γ = 65.17
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 2012-01-06 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 1.63 61.41 92.9 0.05 0.063 10.93 2.35 37403 -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 1.63 1.73 84.3 0.31 0.4 2.49 2.15
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 (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 1DSU 1.8 35.6 26852 1414 94.82 0.2035 0.202 0.2031 0.2312 0.2354 RANDOM 25.871
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] -0.02 0.04 -0.03 0.13 0.06 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.838 r_dihedral_angle_4_deg 19.976 r_dihedral_angle_3_deg 19.052 r_mcangle_it 4.283 r_mcbond_it 3.47 r_dihedral_angle_1_deg 3.391 r_mcbond_other 3.283 r_angle_other_deg 2.496 r_angle_refined_deg 1.921 r_chiral_restr 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.838 r_dihedral_angle_4_deg 19.976 r_dihedral_angle_3_deg 19.052 r_mcangle_it 4.283 r_mcbond_it 3.47 r_dihedral_angle_1_deg 3.391 r_mcbond_other 3.283 r_angle_other_deg 2.496 r_angle_refined_deg 1.921 r_chiral_restr 0.146 r_bond_other_d 0.035 r_bond_refined_d 0.016 r_gen_planes_other 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3362 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing