5NAW

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]


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BIO1TACE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29827% PEG 3350 100 mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.141.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.862α = 90
b = 49.444β = 106.51
c = 39.238γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99999SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2553.5697.70.03217.822.8855553-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.2884.50.3262.241.88

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1TACE1.2526.7852774277897.840.130350.127890.17791RANDOM18.891
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]
0.14-0.26-0.270.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.505
r_sphericity_free32.416
r_dihedral_angle_3_deg14.637
r_dihedral_angle_4_deg14.408
r_sphericity_bonded13.741
r_dihedral_angle_1_deg6.744
r_long_range_B_refined5.813
r_long_range_B_other5.811
r_rigid_bond_restr5.628
r_scangle_other5.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.505
r_sphericity_free32.416
r_dihedral_angle_3_deg14.637
r_dihedral_angle_4_deg14.408
r_sphericity_bonded13.741
r_dihedral_angle_1_deg6.744
r_long_range_B_refined5.813
r_long_range_B_other5.811
r_rigid_bond_restr5.628
r_scangle_other5.114
r_scbond_it4.555
r_scbond_other4.553
r_mcangle_other3.54
r_mcangle_it3.538
r_mcbond_it2.994
r_mcbond_other2.981
r_angle_refined_deg2.521
r_angle_other_deg1.497
r_chiral_restr0.536
r_bond_refined_d0.029
r_gen_planes_refined0.015
r_gen_planes_other0.004
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms1700
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing