5ULG

Crystal structure of RPE65 in complex with MB-008 and palmitate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RSC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.528140% PEG 300, 200 mM NaCl, 100 mM CHES, pH 9.5
Crystal Properties
Matthews coefficientSolvent content
3.1561.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.319α = 90
b = 175.319β = 90
c = 86.653γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97918APS24-ID-E

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
12.150980.1529.34486411

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4RSC2.147.8582511445598.070.177190.175550.20722RANDOM40.86
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]
0.430.210.43-1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.347
r_dihedral_angle_4_deg13.908
r_dihedral_angle_3_deg13.261
r_sphericity_bonded9.058
r_dihedral_angle_1_deg7.093
r_long_range_B_refined6.882
r_long_range_B_other6.882
r_scangle_other5.203
r_mcangle_it3.954
r_mcangle_other3.954
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.347
r_dihedral_angle_4_deg13.908
r_dihedral_angle_3_deg13.261
r_sphericity_bonded9.058
r_dihedral_angle_1_deg7.093
r_long_range_B_refined6.882
r_long_range_B_other6.882
r_scangle_other5.203
r_mcangle_it3.954
r_mcangle_other3.954
r_scbond_it3.358
r_scbond_other3.358
r_mcbond_it2.667
r_mcbond_other2.666
r_angle_refined_deg1.541
r_angle_other_deg0.948
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8154
Nucleic Acid Atoms
Solvent Atoms530
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing