2FR3 | pdb_00002fr3

Crystal Structure of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinoic Acid at 1.48 Angstroms Resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	298	30% (w/v) PEG 4000, 0.1 M sodium citrate/citric acid pH 5.4, and 0.2 ammonium acetate (crystallization performed in dark room and under red light), VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.287	α = 90
b = 46.464	β = 90
c = 77.261	γ = 90

Symmetry
Space Group	P 21 21 21

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		2005-07-23	M	SINGLE WAVELENGTH
2	1	x-ray		M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 32-ID	1.000	APS	32-ID

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
1,2	1.48	39.81	95.5	0.044	28.19		27332	26090			17.1

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)
	1.48	1.53	96.4	96.4	0.139	5.08

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Rigid Body Refinement	THROUGHOUT	1.48	39.81	23523	23523	2622	95.13	0.131	0.131	0.126	0.13	0.174	0.18	RANDOM	15.735

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]
0.45			0.37		-0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.653
r_dihedral_angle_3_deg	11.911
r_dihedral_angle_4_deg	9.076
r_sphericity_free	9.057
r_dihedral_angle_1_deg	6.374
r_scangle_it	5.001
r_sphericity_bonded	4.394
r_scbond_it	3.862
r_mcangle_it	2.875
r_mcbond_it	2.355
r_rigid_bond_restr	1.932
r_angle_refined_deg	1.815
r_angle_other_deg	1.063
r_mcbond_other	0.954
r_symmetry_vdw_other	0.255
r_symmetry_vdw_refined	0.25
r_nbd_refined	0.216
r_nbd_other	0.203
r_xyhbond_nbd_refined	0.192
r_symmetry_hbond_refined	0.186
r_nbtor_refined	0.178
r_chiral_restr	0.131
r_nbtor_other	0.083
r_bond_refined_d	0.019
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	1101
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	26

Software

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