6S5K | pdb_00006s5k

LXRbeta ligand binding domain in complex with small molecule inhibitors

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			100 mM PIPES pH 7 and 17% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.728	α = 90
b = 58.728	β = 90
c = 148.026	γ = 120

Symmetry
Space Group	P 32 2 1

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 210		2005-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.93	ESRF	ID14-2

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	1.6	50.86	96.2	8.3	4.9		187172

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	50.86	38225	1864	95.673	0.182	0.1803	0.19	0.2142	0.22	29.664

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.259
r_dihedral_angle_3_deg	14.652
r_dihedral_angle_4_deg	14.541
r_lrange_it	9.82
r_lrange_other	9.773
r_scangle_other	7.69
r_scangle_it	7.587
r_dihedral_angle_1_deg	5.708
r_scbond_other	5.085
r_scbond_it	5.016
r_mcangle_other	4.715
r_mcangle_it	4.713
r_mcbond_it	3.257
r_mcbond_other	3.252
r_angle_refined_deg	2.351
r_angle_other_deg	1.14
r_symmetry_nbd_refined	0.337
r_nbd_refined	0.263
r_nbtor_refined	0.198
r_nbd_other	0.195
r_xyhbond_nbd_refined	0.165
r_symmetry_nbd_other	0.156
r_chiral_restr	0.139
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_refined	0.059
r_bond_refined_d	0.025
r_symmetry_xyhbond_nbd_other	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1820
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	32

Software

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