8IYT | pdb_00008iyt

Crystal Structure of Serine Palmitoyltransferase complexed with D-methylserine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A2B

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
2.27	45.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.843	α = 90
b = 61.843	β = 90
c = 208.344	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	1.7	50	97.5	0.999	20.5	10.1		44526

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	1.7	1.8			0.999

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	1.7	46.185	44523	4294	97.476	0.178	0.1733	0.19	0.2186	0.23	25.467

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]
1.059			1.059		-2.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.25
r_dihedral_angle_4_deg	18.184
r_dihedral_angle_3_deg	14.378
r_dihedral_angle_1_deg	6.466
r_lrange_it	5.352
r_lrange_other	5.351
r_scangle_it	4.248
r_scangle_other	4.247
r_scbond_it	2.853
r_scbond_other	2.852
r_mcangle_other	2.619
r_mcangle_it	2.618
r_mcbond_other	2.008
r_mcbond_it	2.007
r_angle_refined_deg	1.706
r_angle_other_deg	1.423
r_nbd_refined	0.211
r_symmetry_nbd_other	0.174
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.167
r_nbtor_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.155
r_symmetry_nbd_refined	0.153
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_symmetry_xyhbond_nbd_other	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3031
Nucleic Acid Atoms
Solvent Atoms	384
Heterogen Atoms	39

Software

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