8IYP | pdb_00008iyp

Crystal structure of serine palmitoyltransferase soaked in 190 mM D-serine solution

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
2.2	44.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.975	α = 90
b = 60.975	β = 90
c = 207.311	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 MX225HE		2017-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	0.9	SPring-8	BL38B1

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	1.65	50	99.2	1	38.7	12.9		47801

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	1.65	1.75			0.991

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	1.651	42.248	47801	4946	99.15	0.152	0.1487	0.16	0.1842	0.19	17.502

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]
0.618			0.618		-1.237

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.874
r_dihedral_angle_3_deg	14.889
r_dihedral_angle_1_deg	6.322
r_dihedral_angle_2_deg	6.237
r_lrange_it	5.286
r_lrange_other	5.286
r_scangle_it	4.003
r_scangle_other	4.002
r_scbond_it	2.687
r_scbond_other	2.686
r_mcangle_it	2.117
r_mcangle_other	2.117
r_angle_refined_deg	1.682
r_mcbond_it	1.597
r_mcbond_other	1.597
r_angle_other_deg	0.569
r_nbd_refined	0.233
r_chiral_restr_other	0.222
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.163
r_nbd_other	0.162
r_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.131
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.016
r_xyhbond_nbd_other	0.011
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
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	407
Heterogen Atoms	50

Software

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