2XRX | pdb_00002xrx

CRYSTAL STRUCTURE OF BIPHENYL DIOXYGENASE IN COMPLEX WITH BIPHENYL FROM BURKHOLDERIA XENOVORANS LB400

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XR8	PDB ENTRY 2XR8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		PROTEIN WAS CRYSTALLIZED FROM 20% PEG 5000MME, 50 MM PIPES, PH 6.5.

Crystal Properties
Matthews coefficient	Solvent content
2.4	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.824	α = 102.65
b = 132.646	β = 101.11
c = 130.423	γ = 105.31

Symmetry
Space Group	P 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 SX-165		2004-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B		APS	14-ID-B

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	2.4	100	93	0.06	13.8	2.7		309885		2.2	49.4

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	2.4	2.48	74		0.27	2.2	1.2

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	PDB ENTRY 2XR8	2.42	119.52	291398	3001	95.05	0.23302	0.23264	0.24	0.27031	0.27	RANDOM	44.677

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]
-0.43	-0.05	0.04	-0.64	1.09	1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.418
r_dihedral_angle_3_deg	14.553
r_dihedral_angle_4_deg	13.899
r_dihedral_angle_1_deg	5.168
r_angle_refined_deg	0.905
r_scangle_it	0.705
r_scbond_it	0.486
r_mcangle_it	0.448
r_mcbond_it	0.301
r_nbtor_refined	0.297
r_symmetry_hbond_refined	0.215
r_nbd_refined	0.162
r_symmetry_vdw_refined	0.123
r_xyhbond_nbd_refined	0.113
r_metal_ion_refined	0.095
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	59079
Nucleic Acid Atoms
Solvent Atoms	694
Heterogen Atoms	204

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing