1KW3 | pdb_00001kw3

Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.76	α = 90
b = 121.76	β = 90
c = 108.91	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		2000-11-11	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	20.29	99.9	0.081	0.081	5	11.7	72106	72066

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		0.393	0.393	1.9	9.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	68425	68425	3641	99.87	0.16213	0.16213	0.16137	0.17	0.17653	0.18	RANDOM	11.583

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	18.131
r_dihedral_angle_1_deg	5.131
r_scangle_it	2.792
r_sphericity_free	2.198
r_scbond_it	1.72
r_angle_other_deg	1.571
r_angle_refined_deg	1.439
r_mcangle_it	1.194
r_symmetry_hbond_refined	0.707
r_mcbond_it	0.658
r_symmetry_vdw_other	0.302
r_symmetry_vdw_refined	0.243
r_nbd_refined	0.21
r_nbtor_other	0.203
r_nbd_other	0.196
r_xyhbond_nbd_other	0.14
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
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	300
Heterogen Atoms	17

Software

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