5UL5

Crystal structure of RPE65 in complex with MB-004 and palmitate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP28140% PEG 300, 200 mM NaCl, 100 mM CHES, pH 9.5
Crystal Properties
Matthews coefficientSolvent content
3.1661.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.73α = 90
b = 175.73β = 90
c = 86.37γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97919APS24-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
12.2501000.20911.312.177111

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 SYNTHESISTHROUGHOUT4RSC2.247.8873171393899.980.172360.170340.20942RANDOM43.849
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]
0.080.040.08-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.24
r_dihedral_angle_4_deg16.38
r_dihedral_angle_3_deg13.006
r_sphericity_bonded12.067
r_dihedral_angle_1_deg7.25
r_long_range_B_refined6.566
r_long_range_B_other6.556
r_scangle_other5.091
r_mcangle_it4.09
r_mcangle_other4.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.24
r_dihedral_angle_4_deg16.38
r_dihedral_angle_3_deg13.006
r_sphericity_bonded12.067
r_dihedral_angle_1_deg7.25
r_long_range_B_refined6.566
r_long_range_B_other6.556
r_scangle_other5.091
r_mcangle_it4.09
r_mcangle_other4.09
r_scbond_it3.357
r_scbond_other3.356
r_mcbond_it2.809
r_mcbond_other2.809
r_angle_refined_deg1.551
r_angle_other_deg0.957
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.007
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8261
Nucleic Acid Atoms
Solvent Atoms447
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing