3U2K | pdb_00003u2k

S. aureus GyrB ATPase domain in complex with a small molecule inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop, inhibitor soak	7.5	293	19-30% PEG3350, 0.1MHepes, pH 7.5, 0.2M MgCl2, sitting drop, inhibitor soak, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.175	α = 90
b = 55.497	β = 100.67
c = 51.349	γ = 90

Symmetry
Space Group	C 1 2 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	RIGAKU SATURN 944	mirrors	2010-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.64	35.175	88.3	0.024	21.8	2.7	124850	43084	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.73	72.6		0.18	0.18	4.4	1.9	5136

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 (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	1.64	35.17	42877	2181	88.15	0.1575	0.1562	0.16	0.182	0.19	RANDOM	16.4114

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]
-0.13		-0.19	0.11		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.629
r_dihedral_angle_4_deg	15.928
r_dihedral_angle_3_deg	12.12
r_dihedral_angle_1_deg	5.265
r_scangle_it	3.237
r_scbond_it	1.869
r_angle_refined_deg	1.062
r_mcangle_it	0.968
r_angle_other_deg	0.769
r_mcbond_it	0.485
r_mcbond_other	0.108
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3058
Nucleic Acid Atoms
Solvent Atoms	440
Heterogen Atoms	60

Software

Software
Software Name	Purpose
d*TREK	data scaling
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XDS	data reduction