3IA8 | pdb_00003ia8

The structure of the C-terminal heme nitrobindin domain of THAP domain-containing protein 4 from Homo sapiens

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	Protein Solution (10 mg/ml MSE protein, 0.05 M NaCl, 0.0003 M TCEP, 0.005 M HEPES pH 5) mixed in a 1:1 ratio with the Well Solution (55% Polypropylene glycol 400, 0.1 M Triethanolamine pH 7.5). Cryoprotected with 55% Polypropylene glycol 400, 0.1 M Triethanolamine pH 7.5, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.16	49.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.933	α = 90
b = 74.694	β = 90
c = 103.064	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 300 mm CCD	mirrors and beryllium lenses	2009-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

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	1.79	50	95.9	0.093	9.5	5.8		29918			19.36

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)
	1.79	1.84	76.2		0.457		4.8	1557

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	1.792	35.113	1.34	29830	1510	95.69	0.167	0.165	0.1752	0.201	0.2067	24.305

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]
-0.125			-3.259		-2.01

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.337
f_angle_d	1.449
f_chiral_restr	0.09
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2568
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	86

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

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.