6ULD | pdb_00006uld

Crystal structure of serine hydroxymethyltransferase from Mycobacterium tuberculosis with bound PLP forming a Schiff base with substrate Serine in one monomer and PLP forming a Schiff base with product Glycine in the other monomer

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H7F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	287	MytuD.00783.a.A1.PS00175 at 20.2 mg/ml, incubated with 5 mM pyrazinoic acid, mixed 1:1 with 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M MES/imidazole, pH=6.5, 0.02 M of sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine. Tray: 311079g8, puck: ved0-8

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.65	α = 90
b = 60.01	β = 92.993
c = 101.66	γ = 90

Symmetry
Space Group	P 1 21 1

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	RAYONIX MX-300	Beryllium Lenses	2019-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.5	50	99.1	0.04	0.046	0.999	18.62	4.088		121439			25.784

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.54	93.7		0.517	0.614	0.785	2.23	3.355

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3H7F	1.5	38.76	1.35	121428	2036	99.07	0.1263	0.1256	0.1631	23.75

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
f_dihedral_angle_d	15.703
f_angle_d	0.8272
f_chiral_restr	0.0492
f_plane_restr	0.0055
f_bond_d	0.0052

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6311
Nucleic Acid Atoms
Solvent Atoms	594
Heterogen Atoms	58

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	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.