2R1P | pdb_00002r1p

OpdA from Agrobacterium radiobacter with bound product diethyl thiophosphate from co-crystallisation with tetraethyl dithiopyrophosphate- 1.8 A

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	20% PEG 3350, 0.2M sodium nitrate, pH7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.876	α = 90
b = 108.876	β = 90
c = 62.839	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	2006-05-03	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	95.8			40072	38340

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	94.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY2D2J	1.8	20	40005	36530	1807	95.83	0.16362	0.16208	0.16	0.19505	0.19	RANDOM	18.562

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]
-1.03	-0.52		-1.03		1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.37
r_dihedral_angle_4_deg	16.239
r_dihedral_angle_3_deg	12.965
r_dihedral_angle_1_deg	6.793
r_scangle_it	5.694
r_scbond_it	4.121
r_mcangle_it	2.511
r_mcbond_it	2.04
r_angle_refined_deg	1.618
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.37
r_dihedral_angle_4_deg	16.239
r_dihedral_angle_3_deg	12.965
r_dihedral_angle_1_deg	6.793
r_scangle_it	5.694
r_scbond_it	4.121
r_mcangle_it	2.511
r_mcbond_it	2.04
r_angle_refined_deg	1.618
r_nbtor_refined	0.311
r_nbd_refined	0.235
r_symmetry_vdw_refined	0.195
r_chiral_restr	0.151
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.097
r_metal_ion_refined	0.036
r_bond_refined_d	0.021
r_gen_planes_refined	0.018

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2506
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	15

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.