8H1W | pdb_00008h1w

Serine Palmitoyltransferase from Sphingobacterium multivorum

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	PEG4000, sodium acetate, Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.612	α = 90
b = 61.612	β = 90
c = 208.349	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	CCD	RAYONIX MX225-HS		2018-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	0.9	SPring-8	BL26B2

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	1.4	50	100	1	20.6	10.8		80227

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	1.4	1.48			0.848

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	1.4	43.604	80166	8179	99.973	0.172	0.1685	0.17	0.2017	0.2	21.099

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]
0.468			0.468		-0.936

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.929
r_dihedral_angle_3_deg	14.371
r_dihedral_angle_4_deg	11.422
r_dihedral_angle_1_deg	6.567
r_lrange_it	5.484
r_lrange_other	5.484
r_scangle_it	3.872
r_scangle_other	3.871
r_scbond_it	2.736
r_scbond_other	2.736
r_mcangle_it	2.084
r_mcangle_other	2.084
r_angle_refined_deg	1.895
r_angle_other_deg	1.564
r_mcbond_it	1.548
r_mcbond_other	1.547
r_nbd_refined	0.228
r_symmetry_nbd_refined	0.196
r_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.181
r_symmetry_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.171
r_nbd_other	0.168
r_symmetry_xyhbond_nbd_other	0.112
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3050
Nucleic Acid Atoms
Solvent Atoms	534
Heterogen Atoms	28

Software

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