2OD0

The crystal structure of gene product VP1028 from Vibrio parahaemolyticus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	2 M Ammonium sulfate, 0.1 M Citrate buffer, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.458	α = 90
b = 42.876	β = 90
c = 157.9	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 315	mirrors	2006-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97980	APS	19-ID

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	1.95	79.06	99.44	0.108	20	8.3	20721	20605		2	26.8

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	1.95	2	97.16		0.494	2.1	6.7	1549

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.95	79.06	20605	20605	1091	99.44	0.20187	0.19965	0.24521	RANDOM	26.353

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]
0.87			0.35		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.826
r_dihedral_angle_3_deg	14.54
r_dihedral_angle_4_deg	8.087
r_dihedral_angle_1_deg	5.156
r_scangle_it	3.664
r_scbond_it	2.738
r_mcangle_it	1.546
r_angle_refined_deg	1.38
r_mcbond_it	1.37
r_angle_other_deg	0.88
r_symmetry_vdw_refined	0.322
r_symmetry_hbond_refined	0.261
r_nbd_refined	0.227
r_mcbond_other	0.225
r_symmetry_vdw_other	0.191
r_nbd_other	0.182
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.157
r_metal_ion_refined	0.128
r_nbtor_other	0.086
r_chiral_restr	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1640
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building