6LD8

Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with aminoacrylate and cysteine

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	0.12 M Ethylene Glycols Mix, 0.1 M Na HEPES/MOPS pH 7.5, 10%(w/v) PEG 4000, 20%(v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
4.93	75.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.985	α = 90
b = 161.985	β = 90
c = 245.18	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		2012-12-21	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	2.3	50	99.94	0.12	23.5	7.3		137559

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	2.31	2.39			0.54

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6LD7	2.31	40.61	131279	6941	99.95	0.167	0.1655	0.1945	RANDOM	32.296

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.965
r_dihedral_angle_4_deg	21.729
r_dihedral_angle_3_deg	18.047
r_dihedral_angle_1_deg	7.376
r_angle_refined_deg	1.901
r_angle_other_deg	1.459
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.965
r_dihedral_angle_4_deg	21.729
r_dihedral_angle_3_deg	18.047
r_dihedral_angle_1_deg	7.376
r_angle_refined_deg	1.901
r_angle_other_deg	1.459
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11491
Nucleic Acid Atoms
Solvent Atoms	597
Heterogen Atoms	84

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.