5UL5

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		281	40% PEG 300, 200 mM NaCl, 100 mM CHES, pH 9.5

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.06

Crystal Data

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

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2015-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97919	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	50	100	0.209	11.3	12.1		77111

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	4RSC	2.2	47.88	73171	3938	99.98	0.17236	0.17034	0.20942	RANDOM	43.849

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]
0.08	0.04		0.08		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.24
r_dihedral_angle_4_deg	16.38
r_dihedral_angle_3_deg	13.006
r_sphericity_bonded	12.067
r_dihedral_angle_1_deg	7.25
r_long_range_B_refined	6.566
r_long_range_B_other	6.556
r_scangle_other	5.091
r_mcangle_it	4.09
r_mcangle_other	4.09
r_scbond_it	3.357
r_scbond_other	3.356
r_mcbond_it	2.809
r_mcbond_other	2.809
r_angle_refined_deg	1.551
r_angle_other_deg	0.957
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	8261
Nucleic Acid Atoms
Solvent Atoms	447
Heterogen Atoms	109

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing