6LGO | pdb_00006lgo

Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with homolanthionine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LD7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	287	0.12M Ethylene Glycols Mix, 0.1M Na HEPES/MOPS pH 7.5, 10%(w/v) PEG 4000, 20%(v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
4.87	74.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.222	α = 90
b = 161.222	β = 90
c = 244.914	γ = 90

Symmetry
Space Group	I 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 315r		2013-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	1.0	PAL/PLS	5C (4A)

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	2.39	50	96.15	0.083	8.1	7.3		117802

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	2.39	2.48			0.26

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	6LD7	2.39	47.07	111910	5900	96.19	0.1551	0.1537	0.16	0.1813	0.19	RANDOM	29.899

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]
0.05			0.05		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.776
r_dihedral_angle_4_deg	21.447
r_dihedral_angle_3_deg	18.307
r_dihedral_angle_1_deg	7.441
r_angle_refined_deg	2.427
r_angle_other_deg	1.602
r_chiral_restr	0.122
r_bond_refined_d	0.019
r_gen_planes_refined	0.014
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.776
r_dihedral_angle_4_deg	21.447
r_dihedral_angle_3_deg	18.307
r_dihedral_angle_1_deg	7.441
r_angle_refined_deg	2.427
r_angle_other_deg	1.602
r_chiral_restr	0.122
r_bond_refined_d	0.019
r_gen_planes_refined	0.014
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11484
Nucleic Acid Atoms
Solvent Atoms	397
Heterogen Atoms	116

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
PDB_EXTRACT	data extraction
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.