4CSB

Structure of the Virulence-Associated Protein VapD from the intracellular pathogen Rhodococcus equi.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		PROTEIN:20 MG ML-1 VAPD-CORE IN 20 MM HEPES PH 7.5, 500 MM NACL RESERVOIR: 2.2M AMMONIUM SULPHATE, 0.2M SODIUM THIOCYANATE, 0.1% WV-1 BETA-D-OCTYL GLUCOSIDE

Crystal Properties
Matthews coefficient	Solvent content
2.2	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.844	α = 90
b = 142.844	β = 90
c = 142.844	γ = 90

Symmetry
Space Group	F 4 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	MIRRORS	2013-03-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	1.9	82.5	100	0.09	21	11.9		10376

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	1.9	1.94	100		0.83	3.7	12

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	SAD	THROUGHOUT	NONE	1.9	82.47	9823	497	99.54	0.16077	0.15923	0.19078	RANDOM	28.742

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.302
r_dihedral_angle_3_deg	15.025
r_dihedral_angle_4_deg	8.236
r_dihedral_angle_1_deg	6.326
r_mcangle_it	4.283
r_scbond_it	4.231
r_mcbond_it	2.968
r_mcbond_other	2.881
r_angle_refined_deg	2.141
r_angle_other_deg	1.711
r_chiral_restr	0.224
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	857
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing