2G7B

Crystal Structure of the R132K:R111L:L121E mutant of Cellular Retinoic Acid Binding Protein Type II In Complex With All-Trans-Retinal At 1.18 Angstroms Resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	277	18% (w/v) PEG 6000 and 0.1 M sodium acetate pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.459	α = 90
b = 45.514	β = 90
c = 77.747	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		2004-06-19	M	SINGLE WAVELENGTH
2	1

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	1.18	40	96.7	0.072	25.6		54241	52457		-3

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)
	1.18	1.22	74.6	74.6	0.332

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	1.18	22.81	52405	52405	2920	96.71	0.13	0.13	0.129	0.155	RANDOM	12.18

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]
0.31			0.2		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.278
r_dihedral_angle_4_deg	10.899
r_dihedral_angle_3_deg	10.44
r_sphericity_free	9.638
r_dihedral_angle_1_deg	7.047
r_scangle_it	5.242
r_sphericity_bonded	4.631
r_scbond_it	3.668
r_mcangle_it	2.866
r_rigid_bond_restr	1.949
r_mcbond_it	1.917
r_angle_refined_deg	1.795
r_angle_other_deg	1.585
r_mcbond_other	0.952
r_symmetry_vdw_refined	0.417
r_metal_ion_refined	0.362
r_nbd_refined	0.333
r_symmetry_vdw_other	0.288
r_nbd_other	0.241
r_symmetry_hbond_refined	0.21
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.122
r_nbtor_other	0.088
r_bond_refined_d	0.019
r_gen_planes_other	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1146
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	22

Software

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