5M26 | pdb_00005m26

Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 in complex with methylhydroquinone

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5M21

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	296	14% PEG 3350, 0.35 M MgCl2 and 0.1 M Mes

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.406	α = 90
b = 125.231	β = 102.55
c = 91.352	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 2M		2016-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.0000	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.9	46.694	97.5	0.123	0.994	10.43	4.84		149371		-3	24.408

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2.01	94.8		0.604	0.797	2.72

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	5M21	1.9	30	141943	7452	97.54	0.1628	0.1604	0.16	0.2074	0.21	RANDOM	21.792

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]
-1.01		0.68	-0.39		0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.759
r_dihedral_angle_4_deg	19.557
r_dihedral_angle_3_deg	13.952
r_dihedral_angle_1_deg	6.592
r_mcangle_it	1.696
r_scbond_it	1.66
r_angle_refined_deg	1.414
r_mcbond_it	1.073
r_chiral_restr	0.102
r_bond_refined_d	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.759
r_dihedral_angle_4_deg	19.557
r_dihedral_angle_3_deg	13.952
r_dihedral_angle_1_deg	6.592
r_mcangle_it	1.696
r_scbond_it	1.66
r_angle_refined_deg	1.414
r_mcbond_it	1.073
r_chiral_restr	0.102
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15307
Nucleic Acid Atoms
Solvent Atoms	2035
Heterogen Atoms	38

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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.