7LHJ | pdb_00007lhj

Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A mutant of cellular retinol binding protein II complex with 15-cis-retinal

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	30% PEG 4000, 0.1 M sodium acetate, 0.1 M ammonium acetate pH 4.6, evaporation, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.923	α = 86.203
b = 36.038	β = 86.555
c = 64.026	γ = 65.059

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 300 mm plate		2019-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.000	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	1.26	29.48	88.28	0.107	0.06	13	3.1		58186			13.07

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.26	1.31	88.93		0.291	0.163	4.33

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4QYN	1.26	22.32	1.96	58153	1960	86.22	0.1895	0.1886	0.19	0.2171	0.22	18.49

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.5266
f_angle_d	0.7464
f_chiral_restr	0.0771
f_bond_d	0.0053
f_plane_restr	0.0038

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2184
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	54

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction
Coot	model building
HKL-2000	data processing
HKL-2000	data reduction

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 R01GM157729.