3E6G

Crystal structure of XometC, a cystathionine c-lyase-like protein from Xanthomonas oryzae pv.oryzae

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I87	PDB ENTRY 2I87

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	283	25% PEG3350, 0.2M lithium sulfate monohydrate, 0.1M bis-Tris, pH5.5, sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.351	α = 90
b = 78.351	β = 90
c = 300.989	γ = 90

Symmetry
Space Group	P 41

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 270		2008-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.00000	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	50	100				44441	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.9	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2I87	2.8	42.26	42154	42154	2238	99.98	0.21957	0.21957	0.21559	0.29549	RANDOM	52.296

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.494
r_dihedral_angle_3_deg	22.215
r_dihedral_angle_4_deg	20.566
r_dihedral_angle_1_deg	7.542
r_scangle_it	2.955
r_scbond_it	1.82
r_angle_refined_deg	1.806
r_mcangle_it	1.392
r_mcbond_it	0.77
r_symmetry_hbond_refined	0.428

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.494
r_dihedral_angle_3_deg	22.215
r_dihedral_angle_4_deg	20.566
r_dihedral_angle_1_deg	7.542
r_scangle_it	2.955
r_scbond_it	1.82
r_angle_refined_deg	1.806
r_mcangle_it	1.392
r_mcbond_it	0.77
r_symmetry_hbond_refined	0.428
r_nbtor_refined	0.317
r_nbd_refined	0.26
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_refined	0.179
r_chiral_restr	0.12
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10559
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.