4DUH | pdb_00004duh

Crystal structure of 24 kDa domain of E. coli DNA gyrase B in complex with small molecule inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KZN	PDB entry 1KZN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.4	293	0.1M MES, 22% PEG 3350, 0.2M NaNO3, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.236	α = 90
b = 51.122	β = 95.68
c = 79.13	γ = 90

Symmetry
Space Group	P 1 21 1

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	RAYONIX MX-225	Mirrors	2011-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	1.5	78.74	99.2	0.051	13.8	7.3	68264	67478	1	1

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	1.5	1.53	99.6		0.476		7.3	3350

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 1KZN	1.5	20	98264	67460	3420	98.87	0.1932	0.1915	0.19	0.2255	0.22	RANDOM	26.9519

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]
-0.66		-0.43	0.46		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.108
r_dihedral_angle_4_deg	17.271
r_dihedral_angle_3_deg	13.738
r_dihedral_angle_1_deg	6.829
r_scangle_it	6.372
r_scbond_it	3.979
r_mcangle_it	2.829
r_mcbond_it	1.747
r_angle_refined_deg	1.528
r_chiral_restr	0.153

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.108
r_dihedral_angle_4_deg	17.271
r_dihedral_angle_3_deg	13.738
r_dihedral_angle_1_deg	6.829
r_scangle_it	6.372
r_scbond_it	3.979
r_mcangle_it	2.829
r_mcbond_it	1.747
r_angle_refined_deg	1.528
r_chiral_restr	0.153
r_bond_refined_d	0.018
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3008
Nucleic Acid Atoms
Solvent Atoms	477
Heterogen Atoms	52

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
PHASER	phasing

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.