4E15 | pdb_00004e15

Crystal structure of kynurenine formamidase conjugated with an inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4E11	PDB ENTRY 4E11

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.1 M HEPES, pH 7.5, 18% PEG4000, 8% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.602	α = 90
b = 76.021	β = 90
c = 210.377	γ = 90

Symmetry
Space Group	C 2 2 21

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 315		2010-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0750	NSLS	X29A

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	1.5	50		0.15	25	14.3	91964	90494

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	1.5	1.55			0.34	4	12.5	7888

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 4E11	1.5	46.7	85145	4501	97.51	0.17235	0.17096	0.1691	0.19808	0.1968	RANDOM	15.872

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]
-0.02			-0.03		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.593
r_dihedral_angle_4_deg	14.202
r_dihedral_angle_3_deg	13.632
r_dihedral_angle_1_deg	6.169
r_scangle_it	5.128
r_scbond_it	3.408
r_mcangle_it	2.086
r_angle_refined_deg	2.07
r_mcbond_it	1.289
r_chiral_restr	0.14
r_bond_refined_d	0.024
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4967
Nucleic Acid Atoms
Solvent Atoms	515
Heterogen Atoms	20

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling