8YR5 | pdb_00008yr5

Crystal structure of E. coli phosphatidylserine synthase in apo state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-P23830-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	297	0.09 M Sodium citrate tribasic dihydrate pH 5.9, 0.09 M Lithium sulfate monohydrate, 0.1 M Sodium malonate pH 7.0, 12.6 % (w/v) polyethylene glycol 4000

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.04	α = 88.24
b = 94.1	β = 87.7
c = 194.75	γ = 60.07

Symmetry
Space Group	P 1

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 9M		2021-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	1.000	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.83	48.64	98.2	0.187	0.207	0.088	0.995	8.1	5.3		135369

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.83	2.88		98	1.86	2.063	0.882	0.36		5.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.83	48.64	129010	6358	98.16	0.24394	0.2419	0.2416	0.28478	0.2795	RANDOM	71.2

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]
-2.13	3.5	-2.14	1.94	-1.01	2.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.865
r_long_range_B_refined	12.763
r_long_range_B_other	12.763
r_scangle_other	9.257
r_mcangle_it	9.243
r_mcangle_other	9.243
r_dihedral_angle_2_deg	7.063
r_dihedral_angle_1_deg	6.844
r_mcbond_it	5.864
r_mcbond_other	5.864
r_scbond_it	5.682
r_scbond_other	5.658
r_angle_refined_deg	1.329
r_angle_other_deg	0.477
r_chiral_restr	0.058
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	43775
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	120

Software

Software
Software Name	Purpose
MxDC	data collection
autoPROC	data processing
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction