7R3B | pdb_00007r3b

S-adenosylmethionine synthetase from Lactobacillus plantarum complexed with AMPPNP, methionine and SAM

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P7L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	50mM CaCl2 0.1M Bis-Tris pH 6.8 32.14% PEG MME 550

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.426	α = 93.82
b = 110.927	β = 104.03
c = 112.661	γ = 99.59

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 EIGER2 S 16M		2019-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.82	29.39	94.6	0.114	0.996	10.2	3.5		61578			65.91

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.82	2.921			0.7	0.706	1.6

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 (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	1P7L	2.82	29.41	58472	3108	94.93	0.16143	0.15563	0.15	0.27492	0.27	RANDOM	68.045

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]
-2.92	-4.73	0.58	-6.27	-1.77	9.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.338
r_dihedral_angle_4_deg	22.277
r_dihedral_angle_3_deg	18.475
r_long_range_B_other	13.343
r_long_range_B_refined	13.34
r_scangle_other	11.997
r_mcangle_other	10.945
r_mcangle_it	10.943
r_scbond_it	9.129
r_scbond_other	9.112
r_mcbond_it	8.322
r_mcbond_other	8.314
r_dihedral_angle_1_deg	7.725
r_rigid_bond_restr	3.237
r_angle_refined_deg	1.546
r_angle_other_deg	1.223
r_chiral_restr	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
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	22380
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	273

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing