3FWA | pdb_00003fwa

Structure of berberine bridge enzyme, C166A variant in complex with (S)-reticuline

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D2J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	298	0.2 M MAGNESIUMCHLORIDE, 30% PEG-4000, 0.1 M TRIS/HCL, pH 8.5, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.87	α = 90
b = 68.87	β = 90
c = 246.46	γ = 90

Symmetry
Space Group	P 41 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	MARMOSAIC 225 mm CCD		2008-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9794	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.496	41.9	97.4	0.053	16.6	8.4	95673	95673			12.78

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.59	91.5		0.233	5.1	6.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MOLECULAR REPLACEMENT	THROUGHOUT	3d2j	1.496	41.892	1.99	95673	95673	4780	98.83	0.162	0.162	0.162	0.16	0.177	0.17	random	18.992

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]
-1.854			-1.854		-1.466

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.276
f_angle_d	1.065
f_chiral_restr	0.067
f_bond_d	0.013
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3925
Nucleic Acid Atoms
Solvent Atoms	639
Heterogen Atoms	131

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	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.