3OOD | pdb_00003ood

Structure of OpdA Y257F mutant soaked with diethyl 4-methoxyphenyl phosphate for 20 hours.

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	6.5	291	14.4 % PEG 8000, 160mM calcium acetate hydrate, 80mM sodium cacodylate, 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109	α = 90
b = 109	β = 90
c = 62	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 IV++	Mirrors	2008-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

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	1.89	50	100	0.051	22.6	7.97	33015	33015

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	1.89	50	100

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2D2J	1.89	17.27	33015	33015	1676	95.91	0.15673	0.15673	0.15478	0.16	0.19493	0.2	RANDOM	17.278

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	31.13
r_dihedral_angle_4_deg	15.988
r_dihedral_angle_3_deg	12.307
r_dihedral_angle_1_deg	6.047
r_scangle_it	3.162
r_scbond_it	1.975
r_angle_refined_deg	1.377
r_mcangle_it	1.107
r_mcbond_it	0.711
r_symmetry_hbond_refined	0.438

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.13
r_dihedral_angle_4_deg	15.988
r_dihedral_angle_3_deg	12.307
r_dihedral_angle_1_deg	6.047
r_scangle_it	3.162
r_scbond_it	1.975
r_angle_refined_deg	1.377
r_mcangle_it	1.107
r_mcbond_it	0.711
r_symmetry_hbond_refined	0.438
r_nbtor_refined	0.307
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.103
r_metal_ion_refined	0.029
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2509
Nucleic Acid Atoms
Solvent Atoms	444
Heterogen Atoms	19

Software

Software
Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

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.