3D96 | pdb_00003d96

Crystal Structure of the R132K:Y134F Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.71 Angstroms Resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	30% (W/V) PEG 4000, 0.1 M TRIS-HCL, 0.2 M SODIUM ACETATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.59	α = 73.9
b = 37.23	β = 74.82
c = 58.77	γ = 87.9

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		2002-11-27	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	1.7	50	89.7	0.052	20.44			26617			21.8

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)
	1.7	1.76	48.9		0.24	1.55

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	1.71	50	25713	2298	86.9	0.16	0.153	0.19	0.222	0.25	RANDOM	28.7411

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]
-0.94	-0.55	0.25	-1.29	-0.25	2.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.474
r_dihedral_angle_3_deg	14.011
r_dihedral_angle_4_deg	10.3
r_sphericity_free	6.7
r_dihedral_angle_1_deg	6.384
r_scangle_it	3.669
r_scbond_it	2.71
r_sphericity_bonded	2.192
r_mcangle_it	1.868
r_angle_refined_deg	1.598
r_mcbond_it	1.542
r_rigid_bond_restr	1.352
r_angle_other_deg	0.807
r_mcbond_other	0.465
r_symmetry_vdw_other	0.229
r_nbd_refined	0.206
r_nbd_other	0.192
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.179
r_symmetry_hbond_refined	0.178
r_chiral_restr	0.093
r_nbtor_other	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
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	2122
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	4

Software

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