8YS9 | pdb_00008ys9

Crystal structure of Phosphatidylethanolamine N-methyltransferase from R. thermophilum complexed with DMPE and SAH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		The phase problem was solved by experimental phasing through single-wavelength anomalous dispersion (SAD) with Crank2 that provided in CCP4Cloud Remote v.1.7.019. The model structure was built by sequential iterative real space model building by Coot and refinement by REFMAC5. The model was later used as search model for molecular replacement with MOLREP to solve the native Rt-PmtA structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.4 M ammonium sulfate, 0.1 M potassium sodium tartrate tetrahydrate, 20% (v/v) polyethylene glycol (PEG) 3350

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.042	α = 90
b = 77.681	β = 90
c = 83.159	γ = 90

Symmetry
Space Group	P 21 21 21

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		2022-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97957	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	1.46	56.77	100	0.105	0.109	0.029	1	13.2	13.5		79982

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	1.463	1.488	100		0.322	0.7	13.4

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.46	56.77	79830	3983	99.8	0.152	0.1647	0.197	0.2013	RANDOM	26

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]
0.32			-0.4		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	16.262
r_long_range_B_other	15.678
r_scangle_other	12.954
r_dihedral_angle_3_deg	11.846
r_dihedral_angle_2_deg	10.75
r_scbond_it	9.25
r_scbond_other	9.217
r_mcangle_it	8.584
r_mcangle_other	8.582
r_mcbond_it	6.508
r_dihedral_angle_1_deg	6.502
r_mcbond_other	6.501
r_rigid_bond_restr	4.594
r_angle_refined_deg	1.782
r_angle_other_deg	0.623
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3239
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms	160

Software

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