5DYR

Structure of virulence-associated protein D (VapD) from Xylella fastidiosa

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	289	20% MPD, 0.1M NaAc pH 4.5, 170mM glycine

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.93	α = 90
b = 107.93	β = 90
c = 53.281	γ = 120

Symmetry
Space Group	P 31 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	MARMOSAIC 225 mm CCD		2009-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.4586	LNLS	W01B-MX2

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	2.2	35.1	85.8	0.218	6.7	11.4		15925

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3	18.69	6117	325	87.34	0.20183	0.19914	0.25306	RANDOM	60.259

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]
0.15			0.15		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.621
r_dihedral_angle_4_deg	19.764
r_dihedral_angle_3_deg	18.487
r_long_range_B_refined	11.037
r_long_range_B_other	11.034
r_mcangle_it	7.778
r_mcangle_other	7.778
r_dihedral_angle_1_deg	7.677
r_scangle_other	6.908
r_mcbond_it	5.107
r_mcbond_other	5.097
r_scbond_it	4.713
r_scbond_other	4.713
r_angle_refined_deg	1.722
r_angle_other_deg	1.069
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1153
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
XDS	data scaling
CNS	data scaling