2PBX | pdb_00002pbx

Vibrio cholerae HapR

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			0.2 M HEPES pH 7.5, 12% (wt/vol) polyethylene glycol 8000, and 5% (vol/vol) ethylene glycol, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.785	α = 90
b = 85.085	β = 90
c = 110.385	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	Toroidal focusing mirror	2005-03-17	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.0093	NSLS	X6A
2	SYNCHROTRON	NSLS BEAMLINE X6A	0.9392, 1.0059	NSLS	X6A

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	2.2	67.2	98.3	0.059	0.06	17.68	5		21439		-3

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	2.2	2.3	99.1		0.206	0.308	5.69	5

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	RIPAS	THROUGHOUT	2.2	19.47	19306	2132	99.06	0.23298	0.22976	0.26	0.2626	0.32	RANDOM	47.294

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]
2.92			-3.28		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.831
r_dihedral_angle_4_deg	25.852
r_dihedral_angle_3_deg	23.001
r_dihedral_angle_1_deg	9.466
r_angle_refined_deg	3.189
r_scangle_it	3.019
r_scbond_it	2.519
r_mcangle_it	1
r_mcbond_it	0.735
r_symmetry_vdw_refined	0.397
r_symmetry_hbond_refined	0.355
r_nbtor_refined	0.339
r_nbd_refined	0.306
r_xyhbond_nbd_refined	0.265
r_chiral_restr	0.202
r_bond_refined_d	0.041
r_gen_planes_refined	0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3234
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
SOLVE	phasing