2GBW | pdb_00002gbw

Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	277.15	20% PEG3350, 1.0 M Sodium Chloride, 0.037M Zinc Chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.958	α = 90
b = 134.958	β = 90
c = 219.887	γ = 120

Symmetry
Space Group	P 31 2 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	CCD	ADSC QUANTUM 4		2004-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00000	APS	17-ID

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	1.7	19.8	95.3	0.083	8.2	4.48	253570	241600

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	1.7	1.76	98.1		0.394	2.9	4.1

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 (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	PDB ENTRY 1NDO	1.7	19.8	253570	229247	12180	95.22	0.19012	0.1881	0.2	0.2283	0.24	RANDOM	28.962

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		0.02		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.181
r_dihedral_angle_4_deg	15.322
r_dihedral_angle_3_deg	13.986
r_dihedral_angle_1_deg	6.845
r_scangle_it	3.476
r_scbond_it	2.544
r_angle_refined_deg	1.629
r_mcangle_it	1.527
r_mcbond_it	1.312
r_angle_other_deg	0.968
r_mcbond_other	0.293
r_metal_ion_refined	0.237
r_symmetry_vdw_other	0.231
r_symmetry_hbond_refined	0.222
r_nbd_other	0.211
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.203
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.179
r_chiral_restr	0.102
r_nbtor_other	0.085
r_xyhbond_nbd_other	0.041
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14987
Nucleic Acid Atoms
Solvent Atoms	1978
Heterogen Atoms	21

Software

Software
Software Name	Purpose
d*TREK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection