4EEJ | pdb_00004eej

Crystal Structure of the Q108K:K40L:T51V:T53C:Y19W:R58W:T29L:Q4R Mutant of Cellular Retinol Binding Protein Type II in Complex with All-trans-Retinal at 1.5 Angstrom Resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RCQ	PDB ENTRY 2RCQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION, RECRYSTALLIZATION	4.6	298	40% PEG4000, 0.1 M sodium acetate trihydrate, pH 4.6, 0.1 M ammonium acetate, EVAPORATION, RECRYSTALLIZATION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.918	α = 86.4
b = 35.756	β = 86.44
c = 64.376	γ = 64.94

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	200	CCD	MARMOSAIC 300 mm CCD	mirror		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.1272	APS	21-ID-D

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	1.501	32.36				39769	39769

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	PDB ENTRY 2RCQ	1.501	32.36	35955	34239	1917	95.23	0.17262	0.17065	0.17	0.20798	0.21	RANDOM	16.834

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
r_dihedral_angle_2_deg	32.88
r_dihedral_angle_4_deg	20.306
r_dihedral_angle_3_deg	13.175
r_dihedral_angle_1_deg	7.412
r_scangle_it	6.115
r_scbond_it	3.986
r_mcangle_it	2.81
r_angle_refined_deg	2.389
r_mcbond_it	1.678
r_chiral_restr	0.153

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.88
r_dihedral_angle_4_deg	20.306
r_dihedral_angle_3_deg	13.175
r_dihedral_angle_1_deg	7.412
r_scangle_it	6.115
r_scbond_it	3.986
r_mcangle_it	2.81
r_angle_refined_deg	2.389
r_mcbond_it	1.678
r_chiral_restr	0.153
r_bond_refined_d	0.027
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2156
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	48

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.