3FEL

Crystal structure of the R132K:R111L:T54E mutant of cellular retinoic acid-binding protein II at 1.85 angstrom resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1M BTP, 30% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.803	α = 75.52
b = 36.678	β = 74.88
c = 56.892	γ = 88.4

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		2007-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97850	APS	21-ID-G

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	1.85	53.2	84.5	0.051	26.6	2.4		18943		1	38.2

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	1.85	1.92	43.3		0.297	2.4	1.7	959

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	1.85	35.49	17972	969	84.57	0.19278	0.19278	0.18974	0.24847	RANDOM	24.122

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]
-1.46	-0.21	0.8	-2.63	1.19	3.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.172
r_dihedral_angle_3_deg	14.219
r_dihedral_angle_4_deg	9.863
r_dihedral_angle_1_deg	5.493
r_mcangle_it	1.38
r_angle_refined_deg	1.238
r_scangle_it	1.06
r_mcbond_it	0.899
r_scbond_it	0.792
r_nbtor_refined	0.325

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.172
r_dihedral_angle_3_deg	14.219
r_dihedral_angle_4_deg	9.863
r_dihedral_angle_1_deg	5.493
r_mcangle_it	1.38
r_angle_refined_deg	1.238
r_scangle_it	1.06
r_mcbond_it	0.899
r_scbond_it	0.792
r_nbtor_refined	0.325
r_symmetry_hbond_refined	0.261
r_symmetry_vdw_refined	0.242
r_xyhbond_nbd_refined	0.234
r_nbd_refined	0.229
r_chiral_restr	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2154
Nucleic Acid Atoms
Solvent Atoms	154
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 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.