3SO7 | pdb_00003so7

Organophoshatedegrading enzyme (OpdA)-phosphate complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	0.4 M sodium potassium tartrate tetrahydrate pH 7.0., VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.189	α = 90
b = 109.189	β = 90
c = 62.932	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++			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	Cu FINE FOCUS	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.2	94.56	100	0.105	0.105	8.3	5.02		22261			26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	100		0.321	0.321	3.6	4.96	2200

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	FOURIER SYNTHESIS	THROUGHOUT	2.2	41.24	21123	1136	99.97	0.17511	0.17203	0.1721	0.23341	0.2345	RANDOM	25.671

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]
-0.15	-0.08		-0.15		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.336
r_dihedral_angle_4_deg	18.101
r_dihedral_angle_3_deg	14.528
r_dihedral_angle_1_deg	6.711
r_scangle_it	4.5
r_scbond_it	2.79
r_angle_refined_deg	1.77
r_mcangle_it	1.537
r_mcbond_it	0.852
r_metal_ion_refined	0.495
r_symmetry_hbond_refined	0.315
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.211
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.111
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
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	2511
Nucleic Acid Atoms
Solvent Atoms	271
Heterogen Atoms	9

Software

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