6YMF | pdb_00006ymf

Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the PLP-Serine external aldimine state

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YMD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	292	0.05 M citric acid, 0.05 M BIS-TRIS propane at pH 5.0 and 16% polyethylene glycol 3350 cocrystallized with 50 mM L-serine

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.888	α = 90
b = 93.888	β = 90
c = 134.683	γ = 120

Symmetry
Space Group	P 31 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 EIGER X 16M		2018-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.63	44.89	99.9	0.045	1	29.5	11.3		86052		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.73	99.3		1.098	0.847	2.1	11.3

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	6YMD	1.63	44.89	85018	1033	99.86	0.1067	0.1064	0.12	0.1298	0.14	RANDOM	35.566

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]
-0.41	-0.2		-0.41		1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	38.705
r_dihedral_angle_2_deg	31.849
r_sphericity_bonded	26.156
r_dihedral_angle_4_deg	17.506
r_dihedral_angle_3_deg	13.257
r_dihedral_angle_1_deg	6.301
r_rigid_bond_restr	4.899
r_angle_refined_deg	1.813
r_angle_other_deg	1.168
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	38.705
r_dihedral_angle_2_deg	31.849
r_sphericity_bonded	26.156
r_dihedral_angle_4_deg	17.506
r_dihedral_angle_3_deg	13.257
r_dihedral_angle_1_deg	6.301
r_rigid_bond_restr	4.899
r_angle_refined_deg	1.813
r_angle_other_deg	1.168
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3207
Nucleic Acid Atoms
Solvent Atoms	401
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
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.