8J9T | pdb_00008j9t

Crystal Structure of GyraseA N-terminal at 2.43A Resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6RKS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG 3500, Tris

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.781	α = 90
b = 154.781	β = 90
c = 108.258	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 EIGER2 X 9M		2023-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.42	134.04	99.1	0.993	8.8	10.1		55446

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	2.42	2.49			0.375

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	2.428	45.93	55206	2005	99.062	0.201	0.1993	0.2	0.2348	0.24	51.717

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]
0.037	0.018		0.037		-0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.387
r_dihedral_angle_6_deg	15.694
r_dihedral_angle_2_deg	12.649
r_dihedral_angle_1_deg	5.227
r_rigid_bond_restr	4.527
r_angle_refined_deg	1.29
r_angle_other_deg	0.623
r_symmetry_xyhbond_nbd_refined	0.397
r_xyhbond_nbd_other	0.386
r_symmetry_nbd_refined	0.285
r_nbd_other	0.26
r_symmetry_nbd_other	0.221
r_nbd_refined	0.202
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.167
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.06
r_symmetry_xyhbond_nbd_other	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_lrange_it
r_lrange_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7702
Nucleic Acid Atoms
Solvent Atoms	627
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
MxCuBE	data collection
Coot	model building