4Z6V | pdb_00004z6v

Structure of H200Q variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-nitrocatechol at 1.37 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	6	293	14% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCL

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.18	α = 90
b = 150.635	β = 90
c = 96.103	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	CCD	ADSC QUANTUM 210		2008-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9334	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.37	45.691	97.9	0.064	0.073	0.035	14.2	4.1	325847	325847

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.37	1.44	95.9		0.786	0.786	0.432	1	4.1	46253

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	1.37	40.35	309539	16249	97.69	0.1206	0.1187	0.12	0.1567	0.16	RANDOM	16.321

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]
-0.03			-0.1		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	32.275
r_sphericity_bonded	10.129
r_rigid_bond_restr	1.975
r_mcangle_it	1.806
r_mcbond_it	1.519
r_mcbond_other	1.517
r_angle_refined_deg	1.357
r_angle_other_deg	0.803
r_chiral_restr	0.087
r_bond_refined_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	32.275
r_sphericity_bonded	10.129
r_rigid_bond_restr	1.975
r_mcangle_it	1.806
r_mcbond_it	1.519
r_mcbond_other	1.517
r_angle_refined_deg	1.357
r_angle_other_deg	0.803
r_chiral_restr	0.087
r_bond_refined_d	0.009
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	11519
Nucleic Acid Atoms
Solvent Atoms	1955
Heterogen Atoms	114

Software

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