4COG | pdb_00004cog

Crystal structure of kynurenine formamidase from Burkholderia cenocepacia

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		KYNURENINE FORMAMIDASE FROM PSEUDOMONAS AERUGINOSA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			293	14 % (W/V) PEG 3350, 5 MM COCL2, 5 MM CDCL2, 5 MM MGCL2 AND 5 MM NICL2. 293 K.

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.859	α = 90
b = 50.12	β = 94.15
c = 135.197	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	PIXEL	DECTRIS PILATUS 6M	MIRRORS	2012-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	1.6	28.37	99.3	0.07	12.8	3.6		134904

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	1.6	1.69	99.8		0.48	3	3.6

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	KYNURENINE FORMAMIDASE FROM PSEUDOMONAS AERUGINOSA	1.6	134.84	128111	6778	99.21	0.15063	0.14886	0.15	0.18431	0.18	RANDOM	18.874

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]
-0.19		-0.04	0.28		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.829
r_dihedral_angle_4_deg	18.843
r_dihedral_angle_3_deg	12.653
r_dihedral_angle_1_deg	6.21
r_scangle_it	3.639
r_mcangle_it	2.684
r_scbond_it	2.601
r_angle_refined_deg	2.422
r_mcbond_it	1.834
r_metal_ion_refined	0.537
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.308
r_nbd_refined	0.26
r_chiral_restr	0.221
r_xyhbond_nbd_refined	0.145
r_symmetry_hbond_refined	0.1
r_bond_refined_d	0.025
r_gen_planes_refined	0.014
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	6212
Nucleic Acid Atoms
Solvent Atoms	1068
Heterogen Atoms	131

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing