4RYX

Crystal structure of RPE65 in complex with emixustat and palmitate, P6522 crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4F3A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.528135% MPD, 200 mM (NH4)2SO4 and 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
3.2361.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.766α = 90
b = 177.766β = 90
c = 86.58γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97920APS24-ID-C

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
125097.70.0810.33.35311253110-3
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)
122.13980.12310.973.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONrigid body refinementTHROUGHOUT4F3A244.155310953109264297.690.166720.164480.2099RANDOM41.771
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]
-0.01-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.115
r_dihedral_angle_3_deg12.675
r_dihedral_angle_4_deg12.134
r_long_range_B_refined7.68
r_long_range_B_other7.54
r_dihedral_angle_1_deg6.693
r_scangle_other5.281
r_mcangle_it4.242
r_mcangle_other4.242
r_scbond_it3.415
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.115
r_dihedral_angle_3_deg12.675
r_dihedral_angle_4_deg12.134
r_long_range_B_refined7.68
r_long_range_B_other7.54
r_dihedral_angle_1_deg6.693
r_scangle_other5.281
r_mcangle_it4.242
r_mcangle_other4.242
r_scbond_it3.415
r_scbond_other3.415
r_mcbond_it2.763
r_mcbond_other2.761
r_angle_refined_deg1.515
r_angle_other_deg0.774
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms4113
Nucleic Acid Atoms
Solvent Atoms391
Heterogen Atoms67

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
REFMACphasing