4WHQ

Alkylperoxo reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	1.2 M Ammonium Sulfate, 2.5 mM 2-mercaptoethanol, 100 mM MES pH 6.5; 2:1 ratio of well sol. to 40 mg/ml protein solution in drop

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.259	α = 90
b = 140.724	β = 90
c = 167.824	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2014-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.78	50	97.7	0.073	0.082	0.036	16.4	4.8		140459

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.81	97.2		0.479	0.547	0.255	0.811		4.1	6929

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.78	39.01	133369	7059	97.53	0.1658	0.1643	0.1951	RANDOM	27.162

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	32.341
r_dihedral_angle_4_deg	15.927
r_dihedral_angle_3_deg	13.882
r_dihedral_angle_1_deg	6.683
r_angle_refined_deg	1.522
r_angle_other_deg	0.818
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.341
r_dihedral_angle_4_deg	15.927
r_dihedral_angle_3_deg	13.882
r_dihedral_angle_1_deg	6.683
r_angle_refined_deg	1.522
r_angle_other_deg	0.818
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10357
Nucleic Acid Atoms
Solvent Atoms	891
Heterogen Atoms	226

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
PDB_EXTRACT	data extraction
HKL-3000	data scaling
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.