4LOG

The crystal structure of the orphan nuclear receptor PNR ligand binding domain fused with MBP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3P0U	pdb id 3P0U (for PNR), pdb id 1OMP (for MBP)
experimental model	PDB	1OMP	pdb id 3P0U (for PNR), pdb id 1OMP (for MBP)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.6	298	PEG6000, pH 5.6, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.435	α = 90
b = 184.936	β = 90
c = 85.97	γ = 90

Symmetry
Space Group	P 21 21 2

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 300 mm CCD		2011-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0	APS	21-ID-D

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	2.7	30	83.8	0.085	20.5		38683	35685	2	2

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	2.7	2.8	67.8		0.0655	2	4.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb id 3P0U (for PNR), pdb id 1OMP (for MBP)	2.7	30	35657	2958	96.5	0.28712	0.28544	0.30744	RANDOM	51.63

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]
-0.59			-0.95		1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.484
r_dihedral_angle_4_deg	17.523
r_dihedral_angle_3_deg	17.114
r_sphericity_free	12.158
r_sphericity_bonded	8.254
r_scangle_it	4.039
r_dihedral_angle_1_deg	3.45
r_rigid_bond_restr	3.397
r_scbond_it	2.793
r_mcangle_it	2.451
r_mcbond_it	1.325
r_angle_refined_deg	1.145
r_angle_other_deg	0.852
r_mcbond_other	0.503
r_chiral_restr	0.061
r_bond_refined_d	0.01
r_bond_other_d	0.006
r_gen_planes_refined	0.006
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6172
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction