6C2Q

Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the PLP-L-Serine Intermediate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JBQ	PDB entry 1JBQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	30% PEG400, 100 mM calcium acetate, 100 mM Tris, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.107	α = 90
b = 81.107	β = 90
c = 208.519	γ = 120

Symmetry
Space Group	P 65 2 2

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		2015-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.17	50	100	0.063	0.066	0.019	12.4	11.2		22476

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.21	100		0.277	0.292	0.093	0.987		9.5

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	PDB entry 1JBQ	2.17	50	21199	1195	99.84	0.1613	0.159	0.2025	RANDOM	31.347

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]
0.18	0.09		0.18		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.515
r_dihedral_angle_4_deg	13.045
r_dihedral_angle_3_deg	12.395
r_dihedral_angle_1_deg	6.044
r_angle_refined_deg	1.389
r_angle_other_deg	0.935
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.515
r_dihedral_angle_4_deg	13.045
r_dihedral_angle_3_deg	12.395
r_dihedral_angle_1_deg	6.044
r_angle_refined_deg	1.389
r_angle_other_deg	0.935
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2675
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	phasing
HKL-2000	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction

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.