6QP1 | pdb_00006qp1

Crystal structure of the PLP-bound C-S lyase in the external aldimine form from Staphylococcus hominis complexed with an inhibitor, L-cycloserine.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DQ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298.15	4% Tacsimate pH 6.0, 12% PEG 3,350 (F1: PEG/ION HT, Hampton Research), 20mM L-cycloserine

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.466	α = 90
b = 115.456	β = 90
c = 118.962	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	PIXEL	DECTRIS PILATUS3 6M		2018-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.42	52.88	99.6	0.103	0.11	0.039	0.997	9.8	7.9		143873

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	1.42	1.44	99.1		2.503	2.673	0.929	0.331		8

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	4DQ6	1.42	51.99	136702	7085	99.5	0.1921	0.1907	0.2	0.2189	0.23	RANDOM	22.723

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]
0.08			1.11		-1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.198
r_dihedral_angle_4_deg	16.51
r_dihedral_angle_3_deg	13.608
r_dihedral_angle_1_deg	7.169
r_angle_refined_deg	1.625
r_angle_other_deg	1.057
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.198
r_dihedral_angle_4_deg	16.51
r_dihedral_angle_3_deg	13.608
r_dihedral_angle_1_deg	7.169
r_angle_refined_deg	1.625
r_angle_other_deg	1.057
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6341
Nucleic Acid Atoms
Solvent Atoms	388
Heterogen Atoms	44

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	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.