4RSC | pdb_00004rsc

Crystal structure of RPE65 in complex with emixustat and palmitate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FSN

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.891	α = 90
b = 175.891	β = 90
c = 86.533	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		2014-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0750	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	50	99.54			139166	139163		-3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3FSN	1.8	47.93	139163	132075	7088	99.54	0.16623	0.16463	0.17	0.19569	0.2	RANDOM	33.394

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]
0.3	0.15		0.3		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.418
r_dihedral_angle_4_deg	14.935
r_dihedral_angle_3_deg	11.926
r_sphericity_bonded	9.203
r_long_range_B_refined	7.703
r_long_range_B_other	7.414
r_dihedral_angle_1_deg	6.684
r_scangle_other	4.991
r_mcangle_it	3.941
r_mcangle_other	3.941
r_scbond_it	3.209
r_scbond_other	3.208
r_mcbond_it	2.681
r_mcbond_other	2.677
r_angle_refined_deg	1.549
r_angle_other_deg	0.918
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8134
Nucleic Acid Atoms
Solvent Atoms	1004
Heterogen Atoms	76

Software

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