Experiment: 30XM

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	30XL	Engineered pyrrolysyl-tRNA synthetase (PylRS) from Methanosarcina mazei

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	100 mM MES, 10% Isopropanol

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.43

Symmetry
Space Group	P 1 21 1

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		2025-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.55	30	95.3	0.054	11.6	3.5		85191

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.65	96.5		0.776	2	3.6

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	1.55	30	80923	4259	95.34	0.18532	0.18377	0.1847	0.21444	0.2161	RANDOM	31.497

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]
-1.09		-0.38	0.69		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.82
r_dihedral_angle_4_deg	13.081
r_dihedral_angle_3_deg	11.57
r_dihedral_angle_1_deg	6.257
r_long_range_B_refined	4.385
r_mcangle_it	2.883
r_scbond_it	2.579
r_mcbond_it	2.202
r_rigid_bond_restr	1.313
r_angle_refined_deg	0.986

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.82
r_dihedral_angle_4_deg	13.081
r_dihedral_angle_3_deg	11.57
r_dihedral_angle_1_deg	6.257
r_long_range_B_refined	4.385
r_mcangle_it	2.883
r_scbond_it	2.579
r_mcbond_it	2.202
r_rigid_bond_restr	1.313
r_angle_refined_deg	0.986
r_chiral_restr	0.08
r_gen_planes_refined	0.005
r_bond_refined_d	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4155
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	70

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

30XM | pdb_000030xm