2FS6

Crystal Structure of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.35 Angstroms Resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	30% (w/v) PEG 8000 (4000), 0.1 M TRIS-HCl pH 8.0 (8.5), and 0.2 M Sodium Acetate, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.449	α = 72.68
b = 37.056	β = 76.37
c = 56.527	γ = 87.28

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	77	CCD	MARRESEARCH		2005-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	1.000	APS	14-ID-B

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	1.35	50	88.4	0.042	14.56	2	56961	50380		-3	15.4

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)
	1.35	1.4	56.5	56.5	0.261	1.77	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	Rigid body refinement	THROUGHOUT	1.35	17.24	50364	50364	5082	88.4	0.154	0.154	0.148	0.204	RANDOM	16.794

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	-0.28	0.3	-0.4	-0.2	1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.191
r_dihedral_angle_4_deg	15.157
r_dihedral_angle_3_deg	12.741
r_sphericity_free	7.239
r_dihedral_angle_1_deg	6.818
r_scangle_it	4.846
r_scbond_it	3.391
r_sphericity_bonded	3.354
r_mcangle_it	2.619
r_rigid_bond_restr	1.996
r_angle_refined_deg	1.775
r_mcbond_it	1.774
r_angle_other_deg	0.898
r_mcbond_other	0.748
r_symmetry_vdw_other	0.26
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.221
r_nbd_other	0.196
r_xyhbond_nbd_refined	0.196
r_symmetry_hbond_refined	0.183
r_nbtor_refined	0.177
r_metal_ion_refined	0.153
r_chiral_restr	0.118
r_nbtor_other	0.085
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2199
Nucleic Acid Atoms
Solvent Atoms	427
Heterogen Atoms	31

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction