3ULH | pdb_00003ulh

Crystal structure of a RNA binding domain of THO complex subunit 4 protein (THOC4) from Homo sapiens at 2.54 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	25.0% Glycerol, 0.6M di-sodium hydrogen phosphate, 0.6M potassium dihydrogen phosphate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.152	α = 90
b = 101.152	β = 90
c = 101.152	γ = 90

Symmetry
Space Group	P 41 3 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	ADSC QUANTUM 315	KOHZU: Double Crystal Si(111)	2011-09-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9537,0.9796,0.9794	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.54	29.2	99.9	0.086	16.6	9.8	6271	6271

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.54	2.61	100		0.011	1.136	2.2	10.3	447

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	MAD	THROUGHOUT	2.54	29.2	6245	289	99.87	0.1819	0.1812	0.18	0.1954	0.2	RANDOM	64.6075

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	40.277
r_dihedral_angle_3_deg	18.993
r_dihedral_angle_4_deg	18.689
r_torsion_it	9.026
r_dihedral_angle_1_deg	5.958
r_angle_it	4.861
r_angle_others	2.978
r_bond_it	2.945
r_angle_refined_deg	1.958
r_angle_other_deg	0.913

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.277
r_dihedral_angle_3_deg	18.993
r_dihedral_angle_4_deg	18.689
r_torsion_it	9.026
r_dihedral_angle_1_deg	5.958
r_angle_it	4.861
r_angle_others	2.978
r_bond_it	2.945
r_angle_refined_deg	1.958
r_angle_other_deg	0.913
r_bond_other	0.65
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	632
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SOLVE	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction

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.