2YFL | pdb_00002yfl

Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran

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		PEG 5000, PIPES PH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.556	α = 90
b = 275.982	β = 117.46
c = 92.057	γ = 90

Symmetry
Space Group	P 1 21 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	MARRESEARCH		2005-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-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	2.6	100	80	0.14	11.9	3.1		97588		1.5	45.3

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	2.6	2.69	49.4		0.51	1.5	1.6

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	2.6	137.36	92527	4927	77.71	0.2182	0.21493	0.22	0.28023	0.28	RANDOM	68.641

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		1.06	-1.12		2.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.285
r_dihedral_angle_3_deg	15.498
r_dihedral_angle_4_deg	13.971
r_dihedral_angle_1_deg	5.196
r_angle_refined_deg	0.913
r_scangle_it	0.711
r_scbond_it	0.424
r_mcangle_it	0.35
r_nbtor_refined	0.298
r_mcbond_it	0.194
r_symmetry_hbond_refined	0.193
r_metal_ion_refined	0.175
r_nbd_refined	0.172
r_symmetry_vdw_refined	0.141
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.063
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	29556
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	58

Software

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