Experiment: 31LC

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	2.0 M ammonium sulphate, 0.1M Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.16

Symmetry
Space Group	P 31 2 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 PILATUS 6M		2024-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.32	59.14	96.8	0.074	1	22.6	18.5		15470

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.32	2.36	100		6.382	0.6	0.6	19.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.52	59.14	12026	529	95.985	0.265	0.2599	0.2599	0.3657	0.3519	70

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]
2.389	1.194		2.389		-7.749

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_2_deg	25.846
r_dihedral_angle_3_deg	19.296
r_lrange_other	14.348
r_lrange_it	14.347
r_dihedral_angle_6_deg	12.011
r_scangle_it	11.261
r_scangle_other	11.261
r_mcangle_other	10.048
r_mcangle_it	10.04
r_dihedral_angle_1_deg	7.857

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_2_deg	25.846
r_dihedral_angle_3_deg	19.296
r_lrange_other	14.348
r_lrange_it	14.347
r_dihedral_angle_6_deg	12.011
r_scangle_it	11.261
r_scangle_other	11.261
r_mcangle_other	10.048
r_mcangle_it	10.04
r_dihedral_angle_1_deg	7.857
r_scbond_it	7.352
r_scbond_other	7.34
r_mcbond_it	6.898
r_mcbond_other	6.891
r_dihedral_angle_2_deg	5.131
r_angle_refined_deg	1.654
r_angle_other_deg	0.651
r_nbd_refined	0.278
r_symmetry_nbd_refined	0.263
r_symmetry_nbd_other	0.229
r_nbd_other	0.215
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.115
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_ext_dist_refined_b

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2352
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	63

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.

31LC | pdb_000031lc