7L0E

Crystal structure of bovine RPE65 in complex with gem-difluoro emixustat and palmitate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		281	30% PEG200, 100 mM Tris pH 8.5, 200 mM ammonium phosphate

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.425	α = 90
b = 175.425	β = 90
c = 86.668	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	PIXEL	DECTRIS EIGER X 16M		2020-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.979180	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.9	50	99.7	0.113	0.999	13.1	10.4		118471			45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2.02			2.482	0.43	0.96

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	1.9	47.87	112436	6033	99.74	0.1782	0.177	0.2008	RANDOM	44.77

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]
0.64	0.32		0.64		-2.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.515
r_dihedral_angle_4_deg	12.431
r_dihedral_angle_3_deg	11.354
r_dihedral_angle_1_deg	7.419
r_angle_refined_deg	1.214
r_angle_other_deg	1.116
r_chiral_restr	0.048
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.515
r_dihedral_angle_4_deg	12.431
r_dihedral_angle_3_deg	11.354
r_dihedral_angle_1_deg	7.419
r_angle_refined_deg	1.214
r_angle_other_deg	1.116
r_chiral_restr	0.048
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8119
Nucleic Acid Atoms
Solvent Atoms	844
Heterogen Atoms	85

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.