8PNA | pdb_00008pna

transcription factor BARHL2 bound to TAATG DNA sequence

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8PM5	chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.8	293	PEG 4000, sodium malonate, sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.853	α = 90
b = 46.881	β = 90
c = 71.758	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	PIXEL	DECTRIS PILATUS 6M		2022-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.45	39.25	99.1	0.081	0.086	0.029	0.999	13.1	7.9		23842

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	1.45	1.47	86.2		1.627	1.907	0.966	0.288		3.3

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.45	39.25	22673	1114	99.08	0.1953	0.1936	0.1936	0.2294	0.2295	RANDOM	22.18

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]
-0.24			0.2		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.463
r_dihedral_angle_3_deg	17.127
r_dihedral_angle_4_deg	16.408
r_dihedral_angle_1_deg	9.99
r_angle_refined_deg	2.513
r_angle_other_deg	1.275
r_chiral_restr	0.215
r_gen_planes_refined	0.016
r_bond_refined_d	0.013
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	570
Nucleic Acid Atoms	486
Solvent Atoms	230
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing