3CWK | pdb_00003cwk

Crystal Structure of the R132K:Y134F:R111L:T54V:L121E Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-trans-Retinoic Acid at 1.57 Angstroms Resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1 M MES, 30% (W/V) PEG 5000, 0.2 M AMMONIUM SULFATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.787	α = 90
b = 44.86	β = 90
c = 77.865	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		2004-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 32-ID		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	1.6	50	99.8	0.05	27.28			21826		-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)
	1.6	1.66	100		0.157

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	1.6	39.47	19203	2110	97.7	0.125	0.12	0.14	0.167	0.17	RANDOM	14.29

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]
0.56			0.13		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.979
r_dihedral_angle_3_deg	12.332
r_dihedral_angle_4_deg	9.868
r_sphericity_free	9.116
r_dihedral_angle_1_deg	6.231
r_scangle_it	5.127
r_scbond_it	3.909
r_sphericity_bonded	3.686
r_mcangle_it	2.57
r_rigid_bond_restr	2.305
r_mcbond_it	2.247
r_angle_refined_deg	1.881
r_angle_other_deg	0.965
r_mcbond_other	0.811
r_symmetry_vdw_other	0.314
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.212
r_nbd_other	0.201
r_xyhbond_nbd_refined	0.193
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.125
r_nbtor_other	0.086
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1146
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing