3D95 | pdb_00003d95

Crystal Structure of the R132K:Y134F:R111L:L121E:T54V Mutant of Apo-Cellular Retinoic Acid Binding Protein Type II at 1.20 Angstroms Resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	298	20% (W/V) PEG 6000, 0.1 M SODIUM ACETATE, 5% ETHANOL, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.591	α = 73.28
b = 36.897	β = 75.91
c = 57.811	γ = 87.76

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		2004-03-02	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	1.2	40	93.8	0.066	18.17			77347			16.6

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)
	1.2	1.24	89.9		0.271	2.55

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	1.2	40	75296	7560	90	0.141	0.138	0.4	0.176	0.4	RANDOM	18.14

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]
-0.44	-0.09	-0.21	-0.23	0.15	0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.908
r_dihedral_angle_4_deg	14.684
r_dihedral_angle_3_deg	9.7
r_sphericity_free	8.028
r_dihedral_angle_1_deg	6.459
r_scangle_it	4.873
r_sphericity_bonded	4.865
r_scbond_it	3.677
r_mcangle_it	2.777
r_mcbond_it	2.398
r_rigid_bond_restr	2.397
r_angle_refined_deg	1.676
r_mcbond_other	0.936
r_angle_other_deg	0.878
r_symmetry_vdw_other	0.257
r_symmetry_vdw_refined	0.24
r_nbd_refined	0.207
r_nbd_other	0.187
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.172
r_symmetry_hbond_refined	0.159
r_chiral_restr	0.112
r_nbtor_other	0.086
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
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	2174
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms

Software

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