4GHH | pdb_00004ghh

Structure of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol at 1.55 Ang resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OJT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM 4-nitrocatechol for 1.5 hours in anaerobic glovebox atmosphere prior to cryo-cooling in liquid nitrogen., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.246	α = 90
b = 150.509	β = 90
c = 96.243	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS 6M		2012-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9801	SOLEIL	PROXIMA 1

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	1.55	48.1	99.9	0.037	12.1	5.9	231042	231042		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.63	99.8		0.413	2	5.3	33407

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	MOLECULAR REPLACEMENT	THROUGHOUT	3OJT	1.55	47.83	219459	11502	99.84	0.12534	0.12326	0.13	0.16466	0.17	RANDOM	19.231

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]
-0.02			0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.79
r_sphericity_free	27.018
r_dihedral_angle_4_deg	18.032
r_dihedral_angle_3_deg	12.239
r_sphericity_bonded	9.753
r_dihedral_angle_1_deg	7.07
r_rigid_bond_restr	2.936
r_angle_refined_deg	1.477
r_angle_other_deg	0.928
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.79
r_sphericity_free	27.018
r_dihedral_angle_4_deg	18.032
r_dihedral_angle_3_deg	12.239
r_sphericity_bonded	9.753
r_dihedral_angle_1_deg	7.07
r_rigid_bond_restr	2.936
r_angle_refined_deg	1.477
r_angle_other_deg	0.928
r_chiral_restr	0.098
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11556
Nucleic Acid Atoms
Solvent Atoms	1594
Heterogen Atoms	146

Software

Software
Software Name	Purpose
MX	data collection
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
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.