4MSO

X-ray crystal structure of a serine hydroxymethyl transferase in apo form from Burkholderia cenocepacia

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DFO	PDB ENTRY 1DFO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	MCSG1 G8: 0.2 M ammonium sulfate, 0.1 M TRIS pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.28	α = 90
b = 72.58	β = 90
c = 182.12	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	100	CCD	MARMOSAIC 300 mm CCD		2013-06-19	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)	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	1.4	50	99.7	0.047	23		144864	144410		-3	20.058

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	1.4	1.44	99.7		0.552	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 1DFO	1.4	47.3	144864	144410	7245	99.68	0.1476	0.1457	0.1824	RANDOM	19.1688

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]
0.06			-0.15		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.039
r_sphericity_bonded	14.545
r_dihedral_angle_4_deg	14.354
r_dihedral_angle_3_deg	11.569
r_dihedral_angle_1_deg	7.389
r_rigid_bond_restr	3.343
r_mcangle_it	2.409
r_mcbond_other	1.963
r_mcbond_it	1.956
r_angle_refined_deg	1.698

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.039
r_sphericity_bonded	14.545
r_dihedral_angle_4_deg	14.354
r_dihedral_angle_3_deg	11.569
r_dihedral_angle_1_deg	7.389
r_rigid_bond_restr	3.343
r_mcangle_it	2.409
r_mcbond_other	1.963
r_mcbond_it	1.956
r_angle_refined_deg	1.698
r_angle_other_deg	0.826
r_chiral_restr	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5698
Nucleic Acid Atoms
Solvent Atoms	754
Heterogen Atoms	19

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.