4O9S | pdb_00004o9s

Crystal structure of Retinol-Binding Protein 4 (RBP4)in complex with a non-retinoid ligand

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	1M ammonium phosphate dibasic, 0.1M imidazole, 0.2M sodium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.737	α = 90
b = 85.737	β = 90
c = 118.806	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2007-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	63	99.9			22054	22050	1	2

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.3	30	20882	1128	99.94	0.23265	0.23116	0.23	0.26072	0.26	RANDOM	31.782

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]
0.35	0.18		0.35		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.745
r_dihedral_angle_3_deg	11.482
r_dihedral_angle_4_deg	11.233
r_dihedral_angle_1_deg	4.429
r_long_range_B_refined	2.19
r_long_range_B_other	2.19
r_angle_refined_deg	1.138
r_angle_other_deg	0.621
r_mcangle_it	0.541
r_mcangle_other	0.541
r_scangle_other	0.337
r_mcbond_it	0.288
r_mcbond_other	0.288
r_scbond_it	0.171
r_scbond_other	0.171
r_chiral_restr	0.05
r_bond_refined_d	0.004
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2822
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	176

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling