3QTD | pdb_00003qtd

Crystal structure of putative modulator of gyrase (PmbA) from Pseudomonas aeruginosa PAO1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.2M Mg Formate, 20% P3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.385	α = 90
b = 116.201	β = 90
c = 253.968	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 315r		2010-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9793	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.7	50	98.1	0.171	0.171	10	5.3	56209	56209		-3	49.6

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)
	2.7	2.75	97.6		0.731	0.731	2.1	5.4	2777

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.7	50	53114	53114	2830	97.5	0.22742	0.22742	0.22461	0.27863	0.2405	RANDOM	27.182

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]
-2.41			5.08		-2.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.416
r_dihedral_angle_4_deg	20.266
r_dihedral_angle_3_deg	15.98
r_dihedral_angle_1_deg	6.162
r_angle_other_deg	4.335
r_angle_refined_deg	1.738
r_chiral_restr	0.121
r_bond_refined_d	0.024
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13195
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	54

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXE	model building
DM	model building
MLPHARE	phasing
RESOLVE	model building
CCP4	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing
CCP4	phasing