9OA5 | pdb_00009oa5

Crystal structure of bovine RPE65 in complex with an emixustat azolog

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% v/v PEG 200, 200 mM (NH4)2HPO4

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.72	α = 90
b = 175.72	β = 90
c = 86.59	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 EIGER2 X 16M		2024-06-30	M	SINGLE WAVELENGTH

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

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	1.75	50	100	0.0108	0.999	14.75	13.1		153073

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	1.75	1.85			3.478	0.218	0.56

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	1.75	47.911	153071	7758	99.975	0.15	0.1479	0.158	0.1812	0.1858	37.232

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]
0.349	0.174		0.349		-1.131

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.08
r_lrange_other	17.066
r_dihedral_angle_6_deg	14.199
r_dihedral_angle_3_deg	10.456
r_scangle_it	9.198
r_scangle_other	9.197
r_mcangle_it	8.096
r_mcangle_other	8.096
r_dihedral_angle_1_deg	7.721
r_scbond_it	5.991
r_scbond_other	5.991
r_dihedral_angle_2_deg	5.744
r_mcbond_it	5.264
r_mcbond_other	5.262
r_rigid_bond_restr	1.956
r_angle_refined_deg	0.934
r_angle_other_deg	0.345
r_nbd_other	0.213
r_nbd_refined	0.194
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.132
r_symmetry_nbd_refined	0.128
r_symmetry_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_1	0.054
r_chiral_restr	0.05
r_symmetry_xyhbond_nbd_other	0.037
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8034
Nucleic Acid Atoms
Solvent Atoms	980
Heterogen Atoms	82

Software

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