6TFI | pdb_00006tfi

PXR IN COMPLEX WITH THROMBIN INHIBITOR COMPOUND 17

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HVL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	1 MICROLITER PROTEIN AT 12.1 MG/ML (IN 20 MILLIMOLAR TRIS PH 7.8, 250 MILLIMOLAR NACL, 2.5 MILLIMOLAR EDTA, 5% (V/V) GLYCEROL, 5 MM DTT), PREINCUBATED WITH 25 MILLIMOLAR COMPOUND 17 (FROM 500 MILLIMOLAR STOCK IN DMSO) for 24 hours at 277 K, MIXED WITH 1 MICROLITER OF RESERVOIR (100 MILLIMOLAR IMIDAZOLE PH 8.0, 20 % (V/V) MPD). CRYO BUFFER 100 MILLIMOLAR IMIDAZOLE PH 8.0, 30 % (V/V) MPD

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.356	α = 90
b = 88.964	β = 90
c = 105.658	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	100	CCD	MARMOSAIC 225 mm CCD		2010-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	CC (Half)	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	1.85	44.48	97.9	0.053	0.059	0.999	17.15	5.07		67925			39.61

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.96	98.7		0.878	0.977	0.668	1.82	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FOURIER SYNTHESIS	THROUGHOUT	3HVL	1.85	44.48	65823	2101	97.9	0.17276	0.17192	0.18	0.19932	0.21	RANDOM	41.918

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]
-0.6			0.25		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.873
r_dihedral_angle_3_deg	14.978
r_dihedral_angle_4_deg	14.137
r_long_range_B_refined	9.443
r_long_range_B_other	9.404
r_scangle_other	6.625
r_dihedral_angle_1_deg	5.192
r_mcangle_it	4.67
r_mcangle_other	4.669
r_scbond_it	4.209
r_scbond_other	4.208
r_mcbond_it	3.081
r_mcbond_other	3.081
r_angle_refined_deg	1.308
r_angle_other_deg	1.265
r_chiral_restr	0.074
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	4847
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	89

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing