1VPB | pdb_00001vpb

CRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF DNA GYRASE (BT3649) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.75 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	7.3	277	0.2M KFormate, 20.0% PEG-3350, No Buffer pH 7.3, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP	7	277	20.0% PEG-6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.541	α = 90
b = 154.968	β = 90
c = 106.12	γ = 90

Symmetry
Space Group	C 2 2 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 315	flat mirror	2004-07-06	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC		2004-09-18	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1
2	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.020035,0.979718,0.979811	ALS	8.3.1

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
1,2	1.74	99	98.69	0.052	30.27	4.73		61062			32.84

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)
1,2	1.74	1.77	86.87		0.428	3.61	3.37	2652

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	MAD	THROUGHOUT	1.75	43.78	57756	3091	99.22	0.17951	0.17822	0.19	0.20393	0.21	RANDOM	34.34

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]
0.26			0.8		-1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.044
r_dihedral_angle_4_deg	21.042
r_dihedral_angle_3_deg	11.442
r_scangle_it	7.32
r_dihedral_angle_1_deg	6.56
r_scbond_it	5.427
r_mcangle_it	3.22
r_mcbond_it	2.324
r_angle_refined_deg	1.644
r_angle_other_deg	0.832
r_mcbond_other	0.593
r_symmetry_vdw_other	0.255
r_nbd_refined	0.206
r_nbtor_refined	0.179
r_nbd_other	0.178
r_xyhbond_nbd_refined	0.139
r_symmetry_hbond_refined	0.107
r_symmetry_vdw_refined	0.104
r_chiral_restr	0.102
r_nbtor_other	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3329
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	8

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement