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Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HFD PDB ENTRY 1HFD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.1 M Tris-HCl, 0.02 M NH4PO4, MPD 50.0% v/v, 0.01 M hexamine cobalt (III) chloride, pH 8.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.77 55.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.048 α = 90 b = 132.048 β = 90 c = 180.288 γ = 90
Symmetry Space Group P 43 21 2
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 MARMOSAIC 325 mm CCD 2009-06-11 SINGLE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
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 2.42 25 98.6 0.099 9.8 4 61198 60502 55.38
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 2.42 2.51 99.5 0.505 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1HFD 2.42 19.84 61198 60373 3064 98.65 0.2149 0.213 0.2155 0.2512 0.2556 RANDOM 53.25
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] 0.9485 0.9485 -1.8969
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.87 t_omega_torsion 3.37 t_angle_deg 1.25 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.87 t_omega_torsion 3.37 t_angle_deg 1.25 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9927 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling BUSTER-TNT refinement PDB_EXTRACT data extraction BUSTER refinement