8H20 | pdb_00008h20

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Glycine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG4000, sodium acetate, Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.573	α = 90
b = 61.573	β = 90
c = 207.774	γ = 90

Symmetry
Space Group	P 41 21 2

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		2019-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

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	1.45	50	100	0.999	22.8	9.6		72011

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	1.45	1.54			0.969

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3A2B	1.45	46.059	72008	7291	99.978	0.192	0.1882	0.19	0.2289	0.23	20.116

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]
0.695			0.695		-1.389

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.003
r_dihedral_angle_3_deg	14.407
r_dihedral_angle_4_deg	12.998
r_dihedral_angle_1_deg	6.451
r_lrange_it	5.249
r_lrange_other	5.248
r_scangle_it	4.141
r_scangle_other	4.14
r_scbond_it	2.734
r_scbond_other	2.733
r_mcangle_it	2.176
r_mcangle_other	2.176
r_angle_refined_deg	1.894
r_mcbond_it	1.652
r_mcbond_other	1.652
r_angle_other_deg	1.532
r_nbd_refined	0.228
r_symmetry_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.18
r_nbd_other	0.172
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.167
r_symmetry_nbd_refined	0.117
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3035
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing