2FS7 | pdb_00002fs7

Crystal Structure of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.55 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, 0.1 M Tris-HCl pH 8.0, and 0.2 M Sodium Acetate, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.475	α = 73.09
b = 37.22	β = 75.74
c = 57.597	γ = 87.22

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
2	1

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	1.55	50	92.3	0.042	23.7	2.2	38968	35956		-3	18.7

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)
	1.55	1.61	68.1	68.1	0.157	3.36	2

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	1.55	50	35954	35954	3595	92.45	0.149	0.149	0.144	0.16	0.201	0.21	RANDOM	18.544

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]
-0.63	-0.76	0.73	-1.11	-0.46	1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.574
r_dihedral_angle_4_deg	19.155
r_dihedral_angle_3_deg	11.864
r_sphericity_free	7.673
r_dihedral_angle_1_deg	6.711
r_scangle_it	4.916
r_scbond_it	3.712
r_sphericity_bonded	3.214
r_mcangle_it	2.515
r_mcbond_it	2.12
r_rigid_bond_restr	2.081
r_angle_refined_deg	1.742
r_angle_other_deg	0.888
r_mcbond_other	0.688
r_symmetry_vdw_other	0.254
r_symmetry_vdw_refined	0.241
r_nbd_refined	0.199
r_nbd_other	0.197
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.179
r_symmetry_hbond_refined	0.17
r_chiral_restr	0.113
r_nbtor_other	0.086
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	2163
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	13

Software

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