9DQA | pdb_00009dqa

Crystal structure of bovine RPE65 in complex with EYE-002

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RSC

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.81	α = 90
b = 175.81	β = 90
c = 86.46	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		2024-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.979460	SSRL	BL12-2

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	2.1	50	98.8	0.153	0.997	8.5	10		87750

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	2.1	2.22			2.025	0.298	0.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.1	47.906	87750	4497	98.77	0.182	0.1801	0.187	0.2089	0.2141	46.496

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]
0.828	0.414		0.828		-2.687

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.373
r_dihedral_angle_3_deg	9.511
r_lrange_it	6.841
r_lrange_other	6.84
r_dihedral_angle_1_deg	6.806
r_dihedral_angle_2_deg	3.992
r_scangle_it	3.581
r_scangle_other	3.581
r_mcangle_other	3.245
r_mcangle_it	3.244
r_scbond_it	2.086
r_scbond_other	2.086
r_mcbond_it	1.9
r_mcbond_other	1.898
r_angle_refined_deg	0.914
r_angle_other_deg	0.334
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.175
r_nbd_refined	0.171
r_nbd_other	0.162
r_symmetry_xyhbond_nbd_refined	0.159
r_symmetry_nbd_refined	0.148
r_xyhbond_nbd_refined	0.124
r_metal_ion_refined	0.096
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_1	0.056
r_chiral_restr	0.047
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8153
Nucleic Acid Atoms
Solvent Atoms	987
Heterogen Atoms	76

Software

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