9MX9 | pdb_00009mx9

Crystal structure of the DNA binding domain of FLI1 (F362A) in complex with a DNA containing two contiguous GGAA sites

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JVT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	294	0.2 M calcium acetate, 0.1 M sodium cacodylate, pH 6.5, 18% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119	α = 90
b = 119	β = 90
c = 95.316	γ = 90

Symmetry
Space Group	I 41 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	100	PIXEL	DECTRIS EIGER X 16M		2020-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.55	50	99.9	0.102	1	24.3	13.1		11403		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.59			0.867

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	PDB entry 5JVT	2.55	37.66	10793	599	99.88	0.20855	0.20628	0.2132	0.24965	0.2553	RANDOM	49.264

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]
-1.55			-1.55		3.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.574
r_dihedral_angle_4_deg	20.235
r_dihedral_angle_3_deg	18.193
r_long_range_B_refined	6.221
r_long_range_B_other	6.158
r_dihedral_angle_1_deg	5.83
r_mcangle_it	4.325
r_mcangle_other	4.322
r_scangle_other	4.253
r_scbond_other	2.563
r_scbond_it	2.562
r_mcbond_it	2.548
r_mcbond_other	2.539
r_angle_other_deg	1.214
r_angle_refined_deg	1.18
r_chiral_restr	0.058
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1500
Nucleic Acid Atoms	608
Solvent Atoms	3
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing