6QMT

Complement factor D in complex with the inhibitor 2-(2-(3'-(aminomethyl)-[1,1'-biphenyl]-3-carboxamido)phenyl)acetic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529325% PEGME 3350, 100 mM Bis-Tris pH 5.5
Crystal Properties
Matthews coefficientSolvent content
1.7128.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.964α = 83.03
b = 39.235β = 75.34
c = 63.502γ = 65.17
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-01-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.6361.4192.90.050.06310.932.3537403-3
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)RedundancyNumber Unique Reflections (All)
11.631.7384.30.310.42.492.15

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 REPLACEMENTTHROUGHOUT1DSU1.835.626852141494.820.20350.2020.2312RANDOM25.871
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]
-0.020.04-0.030.130.06-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.838
r_dihedral_angle_4_deg19.976
r_dihedral_angle_3_deg19.052
r_mcangle_it4.283
r_mcbond_it3.47
r_dihedral_angle_1_deg3.391
r_mcbond_other3.283
r_angle_other_deg2.496
r_angle_refined_deg1.921
r_chiral_restr0.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.838
r_dihedral_angle_4_deg19.976
r_dihedral_angle_3_deg19.052
r_mcangle_it4.283
r_mcbond_it3.47
r_dihedral_angle_1_deg3.391
r_mcbond_other3.283
r_angle_other_deg2.496
r_angle_refined_deg1.921
r_chiral_restr0.146
r_bond_other_d0.035
r_bond_refined_d0.016
r_gen_planes_other0.01
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3362
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing