2D2H | pdb_00002d2h

OpdA from Agrobacterium radiobacter with bound inhibitor trimethyl phosphate at 1.8 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	277	20% PEG 3350, 0.2M NaNO3, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.69	53.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.926	α = 90
b = 108.926	β = 90
c = 62.345	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	173	IMAGE PLATE	RIGAKU RAXIS IIC	Confocal Mirrors	2004-11-12	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	97			39806	38568

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	1.8	1.86	97.3

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 (All)	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	1.8	19.6	36354	34612	1742		0.192	0.18946	0.18818	0.1815	0.2143	0.2111	RANDOM	15.65

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	-0.5		-1		1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.917
r_dihedral_angle_4_deg	14.226
r_dihedral_angle_3_deg	12.515
r_dihedral_angle_1_deg	5.981
r_scangle_it	3.397
r_scbond_it	2.172
r_angle_refined_deg	1.36
r_mcangle_it	1.104
r_mcbond_it	0.919
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.917
r_dihedral_angle_4_deg	14.226
r_dihedral_angle_3_deg	12.515
r_dihedral_angle_1_deg	5.981
r_scangle_it	3.397
r_scbond_it	2.172
r_angle_refined_deg	1.36
r_mcangle_it	1.104
r_mcbond_it	0.919
r_nbtor_refined	0.304
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.168
r_symmetry_vdw_refined	0.164
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2511
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
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.