4RSE

Crystal structure of RPE65 in complex with MB-001 and palmitate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.528140% PEG 300 200 mM NaCl 100 mM CHES-NAOH, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
3.1661.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.639α = 90
b = 175.639β = 90
c = 86.611γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-08-22MSINGLE 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
12.395099.155988159880-3

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 REPLACEMENTTHROUGHOUT3FSN2.3947.95988056801307999.150.197840.195760.2357RANDOM47.059
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]
0.540.270.54-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.122
r_sphericity_bonded18.333
r_dihedral_angle_4_deg17.243
r_dihedral_angle_3_deg13.885
r_dihedral_angle_1_deg6.939
r_long_range_B_refined6.6
r_long_range_B_other6.558
r_scangle_other4.197
r_mcangle_it3.975
r_mcangle_other3.975
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.122
r_sphericity_bonded18.333
r_dihedral_angle_4_deg17.243
r_dihedral_angle_3_deg13.885
r_dihedral_angle_1_deg6.939
r_long_range_B_refined6.6
r_long_range_B_other6.558
r_scangle_other4.197
r_mcangle_it3.975
r_mcangle_other3.975
r_scbond_it2.555
r_scbond_other2.555
r_mcbond_it2.43
r_mcbond_other2.429
r_angle_refined_deg1.398
r_angle_other_deg0.979
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8250
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms82

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
REFMACphasing