6RAV | pdb_00006rav

Complement factor B protease domain in complex with the reversible inhibitor 4-((2S,4S)-4-ethoxy-1-((5-methoxy-7-methyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29324 % (w/v) PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris (pH 5.5), 2mM inhibitor
Crystal Properties
Matthews coefficientSolvent content
2.5451.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.463α = 90
b = 97.446β = 100.475
c = 61.815γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-06-01MSINGLE 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
11.748.72398.80.0680.08110.823.368802-3
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)
11.71.7796.60.8140.9911.83.15

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1dle1.748.72368598343598.4910.1970.19520.210.22670.2431.753
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]
2.5014.074-0.945-2.867
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.263
r_dihedral_angle_3_deg16.208
r_dihedral_angle_4_deg15.273
r_lrange_it6.934
r_lrange_other6.845
r_dihedral_angle_1_deg6.826
r_scangle_it5.27
r_scangle_other5.119
r_mcangle_it3.715
r_mcangle_other3.715
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.263
r_dihedral_angle_3_deg16.208
r_dihedral_angle_4_deg15.273
r_lrange_it6.934
r_lrange_other6.845
r_dihedral_angle_1_deg6.826
r_scangle_it5.27
r_scangle_other5.119
r_mcangle_it3.715
r_mcangle_other3.715
r_scbond_it3.495
r_scbond_other3.393
r_mcbond_it2.544
r_mcbond_other2.543
r_angle_refined_deg1.557
r_angle_other_deg1.322
r_symmetry_xyhbond_nbd_refined0.231
r_nbd_refined0.191
r_nbd_other0.188
r_symmetry_nbd_other0.186
r_symmetry_nbd_refined0.184
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.145
r_ncsr_local_group_10.096
r_symmetry_nbtor_other0.081
r_chiral_restr0.076
r_symmetry_metal_ion_refined0.069
r_xyhbond_nbd_other0.063
r_metal_ion_refined0.037
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4409
Nucleic Acid Atoms
Solvent Atoms366
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing