3C86

OpdA from agrobacterium radiobacter with bound product diethyl thiophosphate from crystal soaking with tetraethyl dithiopyrophosphate- 1.8 A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D2J	PDB ENTRY 2D2J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	20% PEG3350, 0.2M NaNO3, pH7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.918	α = 90
b = 108.918	β = 90
c = 62.648	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	IMAGE PLATE	RIGAKU RAXIS IIC	Confocal Mirrors	2006-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	20	98.9			39491	39491

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.91	93.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2D2J	1.8	20	37486	37486	1977	98.85	0.1631	0.1631	0.16177	0.18683	RANDOM	24.42

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]
-1.42	-0.71		-1.42		2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.159
r_dihedral_angle_4_deg	17.57
r_dihedral_angle_3_deg	12.867
r_dihedral_angle_1_deg	6.846
r_scangle_it	6.15
r_scbond_it	4.305
r_mcangle_it	2.596
r_mcbond_it	1.991
r_angle_refined_deg	1.596
r_nbtor_refined	0.313
r_nbd_refined	0.238
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.148
r_metal_ion_refined	0.132
r_symmetry_hbond_refined	0.104
r_bond_refined_d	0.021
r_gen_planes_refined	0.017
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_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	2504
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing