1PJ7 | pdb_00001pj7

Structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folinic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PJ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	15% PEG 2000MME, 0.2M MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.62	52.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.621	α = 90
b = 223.74	β = 90
c = 119.371	γ = 90

Symmetry
Space Group	C 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	IMAGE PLATE	MARRESEARCH		2002-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.9	EMBL/DESY, HAMBURG	X11

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	2.1	20	88.3	0.073	6.2	2.5	46564	46564

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.15	84.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1PJ6	2.1	20	46564	46564	2482	100	0.16253	0.16253	0.15934	0.16	0.22172	0.22	RANDOM	33.336

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]
-1.02			-0.57		1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	13.771
r_dihedral_angle_1_deg	6.522
r_scangle_it	4.96
r_scbond_it	3.238
r_angle_refined_deg	1.831
r_mcangle_it	1.786
r_mcbond_it	1.037
r_symmetry_hbond_refined	0.353
r_symmetry_vdw_refined	0.263
r_nbd_refined	0.228

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	13.771
r_dihedral_angle_1_deg	6.522
r_scangle_it	4.96
r_scbond_it	3.238
r_angle_refined_deg	1.831
r_mcangle_it	1.786
r_mcbond_it	1.037
r_symmetry_hbond_refined	0.353
r_symmetry_vdw_refined	0.263
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.128
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6237
Nucleic Acid Atoms
Solvent Atoms	778
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.