4RSC

Crystal structure of RPE65 in complex with emixustat and palmitate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FSN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.528130% PEG200 200 mM ammonium phosphate 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
3.1761.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.891α = 90
b = 175.891β = 90
c = 86.533γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0750NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.85099.54139166139163-3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3FSN1.847.93139163132075708899.540.166230.164630.19569RANDOM33.394
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]
0.30.150.3-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.418
r_dihedral_angle_4_deg14.935
r_dihedral_angle_3_deg11.926
r_sphericity_bonded9.203
r_long_range_B_refined7.703
r_long_range_B_other7.414
r_dihedral_angle_1_deg6.684
r_scangle_other4.991
r_mcangle_it3.941
r_mcangle_other3.941
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.418
r_dihedral_angle_4_deg14.935
r_dihedral_angle_3_deg11.926
r_sphericity_bonded9.203
r_long_range_B_refined7.703
r_long_range_B_other7.414
r_dihedral_angle_1_deg6.684
r_scangle_other4.991
r_mcangle_it3.941
r_mcangle_other3.941
r_scbond_it3.209
r_scbond_other3.208
r_mcbond_it2.681
r_mcbond_other2.677
r_angle_refined_deg1.549
r_angle_other_deg0.918
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8134
Nucleic Acid Atoms
Solvent Atoms1004
Heterogen Atoms76

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
REFMACphasing