6FUT

Complement factor D in complex with the inhibitor (S)-3'-(aminomethyl)-N-(1,2,3,4-tetrahydronaphthalen-1-yl)-[1,1'-biphenyl]-3-carboxamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29322-25% PEG3350, 100 mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.0659.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.225α = 90
b = 77.041β = 90
c = 84.898γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2008-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4657.19815.15.6852456
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)
11.461.510.5123.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.557.0545998242198.180.159080.157790.18382RANDOM14.489
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]
-0.06-0.070.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.197
r_dihedral_angle_4_deg17.55
r_dihedral_angle_3_deg12.732
r_dihedral_angle_1_deg6.488
r_long_range_B_refined6.369
r_long_range_B_other6.095
r_scangle_other4.745
r_scbond_it3.145
r_scbond_other3.127
r_angle_refined_deg2.469
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.197
r_dihedral_angle_4_deg17.55
r_dihedral_angle_3_deg12.732
r_dihedral_angle_1_deg6.488
r_long_range_B_refined6.369
r_long_range_B_other6.095
r_scangle_other4.745
r_scbond_it3.145
r_scbond_other3.127
r_angle_refined_deg2.469
r_mcangle_it2.326
r_mcangle_other2.325
r_mcbond_it1.652
r_mcbond_other1.606
r_angle_other_deg1.213
r_chiral_restr0.151
r_bond_refined_d0.026
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1700
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing