2YFJ

Crystal structure of Biphenyl dioxygenase variant RR41 with dibenzofuran

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		PEG 5000 MME AND PIPES PH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.3	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.979	α = 90
b = 278.125	β = 117.65
c = 92.956	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 MX-300		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	2.1	100	93	0.08	16.02	4.5		210175		2	38.2

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	2.1	2.18	80		0.55	2	2.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2XR8	2.15	138.68	186884	9876	92.94	0.20509	0.2036	0.23312	RANDOM	42.576

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]
0.67		0.52	-0.68		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.881
r_dihedral_angle_4_deg	13.537
r_dihedral_angle_3_deg	13.239
r_dihedral_angle_1_deg	4.995
r_angle_refined_deg	0.92
r_scangle_it	0.627
r_scbond_it	0.385
r_mcangle_it	0.302
r_nbtor_refined	0.294
r_mcbond_it	0.17
r_nbd_refined	0.152
r_metal_ion_refined	0.141
r_symmetry_vdw_refined	0.13
r_symmetry_hbond_refined	0.126
r_xyhbond_nbd_refined	0.094
r_chiral_restr	0.059
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	652
Heterogen Atoms	69

Software

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