9N39 | pdb_00009n39

DNA gyrase complexed with uncleaved DNA and Compound 185 to 2.25 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7MVS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	50 mM Bis-Tris pH 6.0, 15.33% PEG5000 MME

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.479	α = 90
b = 93.479	β = 90
c = 410.378	γ = 120

Symmetry
Space Group	P 61

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 PILATUS3 6M		2021-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97911	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.25	23.89	99.1	0.296	0.146	5.4	4.6		93806

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.29	95.8		2.98	2.02		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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.255	23.89	93725	4774	98.704	0.204	0.2017	0.2071	0.2558	0.258	53.617

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]
-1.091	-0.546		-1.091		3.541

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.04
r_dihedral_angle_6_deg	13.923
r_lrange_it	10.224
r_lrange_other	10.224
r_dihedral_angle_2_deg	8.42
r_scangle_it	8.307
r_scangle_other	8.307
r_dihedral_angle_1_deg	7.271
r_mcangle_it	6.103
r_mcangle_other	6.102
r_scbond_it	5.532
r_scbond_other	5.531
r_mcbond_it	4.226
r_mcbond_other	4.226
r_angle_refined_deg	2.084
r_angle_other_deg	0.583
r_dihedral_angle_other_2_deg	0.455
r_symmetry_nbd_refined	0.381
r_nbd_refined	0.224
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.179
r_nbd_other	0.176
r_symmetry_xyhbond_nbd_refined	0.103
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10635
Nucleic Acid Atoms	800
Solvent Atoms	290
Heterogen Atoms	36

Software

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