6YRW

SHMT from Streptococcus thermophilus Tyr55Ser variant as internal aldimine and as non-covalent complex with D-Ser

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	PLP 5mM D-serine 100mM Cacodylate 0.1M ph 6.5 Sodium citrate 0.85M

Crystal Properties
Matthews coefficient	Solvent content
4.24	70.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 199.956	α = 90
b = 113.657	β = 94.13
c = 132.479	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS 2M		2015-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.9697	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.33	47.85	76.01	0.95	41.89	1.59		80329

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.565			0.95

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	4WXG	2.5	47.85	73924	3838	76.01	0.1788	0.1763	0.2265	RANDOM	40.372

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]
-2.82		-3.26	-0.13		3.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.002
r_dihedral_angle_4_deg	16.246
r_dihedral_angle_3_deg	16.187
r_dihedral_angle_1_deg	7.208
r_angle_refined_deg	1.587
r_angle_other_deg	1.286
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.002
r_dihedral_angle_4_deg	16.246
r_dihedral_angle_3_deg	16.187
r_dihedral_angle_1_deg	7.208
r_angle_refined_deg	1.587
r_angle_other_deg	1.286
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12472
Nucleic Acid Atoms
Solvent Atoms	376
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
XPREP	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.