4WNG | pdb_00004wng

Crystal structure of the TPR domain of LGN in complex with Frmpd4/Preso1 at 2.1 Angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WNE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.1 M BisTrispropane (pH 8.0), 0.2 M magnesium chloride, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.527	α = 90
b = 90.527	β = 90
c = 177.067	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS PILATUS 2M-F		2014-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.1000	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.1	50	99.9	0.093	0.096	0.023	8.2	17.5		25343

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	100		0.951	0.985	0.257	0.915	2.308	14.4	1227

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	MOLECULAR REPLACEMENT	THROUGHOUT	4WNE	2.11	38.58	23962	1284	98.99	0.2268	0.2244	0.23	0.2712	0.28	RANDOM	56.444

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]
1.14	1.14		1.14		-3.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.76
r_dihedral_angle_4_deg	15.585
r_dihedral_angle_3_deg	14.925
r_dihedral_angle_1_deg	4.773
r_angle_refined_deg	1.066
r_angle_other_deg	0.704
r_chiral_restr	0.058
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.76
r_dihedral_angle_4_deg	15.585
r_dihedral_angle_3_deg	14.925
r_dihedral_angle_1_deg	4.773
r_angle_refined_deg	1.066
r_angle_other_deg	0.704
r_chiral_restr	0.058
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2607
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.