3TQ6 | pdb_00003tq6

Crystal structure of human mitochondrial transcription factor A, TFAM or mtTFA, bound to the light strand promoter LSP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	293.15	37.5% (v/v) PEG1000, 300 mM sodium chloride, 0.1 M Na,K-phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.9	α = 90
b = 117.2	β = 90
c = 56.53	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 225 mm CCD	Focusing mirrors: one pair of (300x40x15) mm3 long Pt coated Si mirror, 260mm usable, in a Kirkpatrick-Baez geometry;	2010-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.45	40.84	99.8	0.08	0.049	8.2	7		28529	1.5	1.6	59.217

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	2.45	2.57	100		0.467	0.467	4.2	7.4	30350

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.45	40.84	2954	28483	992		0.1832	0.1816	0.19	0.2283	0.24	RANDOM	41.79

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]
3.9362			-8.0574		4.1212

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	20.65
t_it	20
t_gen_planes	5
t_nbd	5
t_chiral_improper_torsion	5
t_ideal_dist_contact	4
t_omega_torsion	2.83
t_dihedral_angle_d	2
t_trig_c_planes	2
t_angle_deg	1.4

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	20.65
t_it	20
t_gen_planes	5
t_nbd	5
t_chiral_improper_torsion	5
t_ideal_dist_contact	4
t_omega_torsion	2.83
t_dihedral_angle_d	2
t_trig_c_planes	2
t_angle_deg	1.4
t_utility_distance	1
t_bond_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3237
Nucleic Acid Atoms	1792
Solvent Atoms	186
Heterogen Atoms	28

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

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.