6BQ9

2.55 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-493) of DNA Topoisomerase IV Subunit A from Pseudomonas putida

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	Protein: 9.5 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: Classics II (C1), 3.5M Sodium formate pH (7.0); Cryo: 4.0M Sodium formate

Crystal Properties
Matthews coefficient	Solvent content
4.16	70.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.494	α = 90
b = 224.057	β = 90
c = 115.747	γ = 90

Symmetry
Space Group	C 2 2 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	C(111)	2017-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	30	99	0.068	0.068	0.074	0.027	28.3	7.4		30230		-3	70.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.59	98.8		0.785	0.785	0.848	0.316	0.903	2.2	6.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5EIX	2.55	29.35	28738	1487	98.4	0.20958	0.20765	0.24654	RANDOM	95.211

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]
10.4			-8.77		-1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.992
r_dihedral_angle_4_deg	10.486
r_dihedral_angle_3_deg	9.379
r_long_range_B_refined	7.329
r_long_range_B_other	7.326
r_scangle_other	4.965
r_mcangle_it	4.814
r_mcangle_other	4.814
r_scbond_it	3.091
r_scbond_other	3.09
r_mcbond_it	3.021
r_mcbond_other	3.003
r_dihedral_angle_1_deg	2.071
r_angle_refined_deg	1.41
r_angle_other_deg	0.89
r_chiral_restr	0.08
r_gen_planes_refined	0.023
r_gen_planes_other	0.02
r_bond_refined_d	0.008
r_bond_other_d	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	3627
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	phasing