3I17

Crystal structure of the apo R132K:L121E mutant of cellular retinoic acid-binding protein II at 1.68 angstrom resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.5	298	0.1 M Bis-tris-propane, pH 9.5, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.699	α = 105.8
b = 37.271	β = 106.44
c = 60.371	γ = 89.97

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	CCD	MARMOSAIC 300 mm CCD		2008-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.99999	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.68	55.56	94.5	0.051	20.8	3.8		30624		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.68	1.724	90.95		0.251	4	4.2	2025

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2G7B	1.68	35.74	29087	1536	96.61	0.18259	0.18259	0.18001	0.23095	RANDOM	30.287

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]
0.23	0.14	1.74	-0.9	-0.11	1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.987
r_dihedral_angle_3_deg	12.138
r_dihedral_angle_4_deg	9.373
r_dihedral_angle_1_deg	5.895
r_mcangle_it	2.182
r_scangle_it	2.056
r_mcbond_it	1.4
r_scbond_it	1.341
r_angle_refined_deg	1.333
r_nbtor_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.987
r_dihedral_angle_3_deg	12.138
r_dihedral_angle_4_deg	9.373
r_dihedral_angle_1_deg	5.895
r_mcangle_it	2.182
r_scangle_it	2.056
r_mcbond_it	1.4
r_scbond_it	1.341
r_angle_refined_deg	1.333
r_nbtor_refined	0.323
r_symmetry_vdw_refined	0.244
r_symmetry_hbond_refined	0.243
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.204
r_chiral_restr	0.091
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2180
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms

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 National Science Foundation (DBI-1832184), 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 R01GM133198.