3PC3 | pdb_00003pc3

Full length structure of cystathionine beta-synthase from Drosophila in complex with aminoacrylate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PC2	PDB entry 3PC2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	298	23% PEG 3350, 0.2 Li2SO4, 100 mM BIS-TRIS 6.5, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.275	α = 90
b = 138.815	β = 90
c = 75.146	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	MARMOSAIC 300 mm CCD	K-B pair of biomorph mirrors for vertical and horizontal focusing	2010-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

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	1.55	50	93.8	0.1	11.2	6.6	70759	66372

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)
	1.55	1.61	67.1		0.546		3.4	4714

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	PHASER	THROUGHOUT	PDB entry 3PC2	1.55	41.45	66337	3348	93.75	0.1503	0.1482	0.15	0.1883	0.19	RANDOM	17.7789

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]
0.51			0.03		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.169
r_dihedral_angle_4_deg	17.191
r_dihedral_angle_3_deg	11.566
r_dihedral_angle_1_deg	5.586
r_scangle_it	3.409
r_scbond_it	2.158
r_mcangle_it	1.478
r_angle_refined_deg	1.179
r_rigid_bond_restr	0.97
r_mcbond_it	0.847

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.169
r_dihedral_angle_4_deg	17.191
r_dihedral_angle_3_deg	11.566
r_dihedral_angle_1_deg	5.586
r_scangle_it	3.409
r_scbond_it	2.158
r_mcangle_it	1.478
r_angle_refined_deg	1.179
r_rigid_bond_restr	0.97
r_mcbond_it	0.847
r_chiral_restr	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3865
Nucleic Acid Atoms
Solvent Atoms	712
Heterogen Atoms	64

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
PHASER	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.