1KW6 | pdb_00001kw6

Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 1.45 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Batch	7.5	285	Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
3.15	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.829	α = 90
b = 121.829	β = 90
c = 109.357	γ = 90

Symmetry
Space Group	I 4 2 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	ADSC QUANTUM 4		2000-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	1.0	Photon Factory	BL-6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.45	26.08	99.9	0.063	0.063	7.8	8.7	72458	72435

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.53	99.9		0.373	0.373	2	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.45	87.71	68780	3654	99.84	0.1634	0.163	0.17	0.17102	0.18	RANDOM	11.595

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.335
r_dihedral_angle_1_deg	4.961
r_scangle_it	2.733
r_angle_other_deg	2.135
r_scbond_it	1.696
r_sphericity_free	1.461
r_angle_refined_deg	1.4
r_mcangle_it	1.125
r_symmetry_hbond_refined	0.654
r_mcbond_it	0.597
r_symmetry_vdw_refined	0.313
r_symmetry_vdw_other	0.23
r_nbd_refined	0.221
r_nbtor_other	0.221
r_nbd_other	0.198
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2229
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	31

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling