Experiment: 23LX

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VH8

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.1 M Sodium citrate tribasic dihydrate pH 5.5, 16% w/v Polyethylene glycol 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.63

Symmetry
Space Group	C 1 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		2024-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97923	SSRF	BL19U1

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	1.7	55.73	99.1	0.115	0.998	12.8	6.3		29555

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	1.7	1.73			0.848	0.513	2.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	55.728	29526	1525	98.944	0.18	0.1776	0.1848	0.2305	0.2397	RANDOM	19.042

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]
3.613		-0.517	-2.707		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.21
r_dihedral_angle_2_deg	16.615
r_dihedral_angle_6_deg	14.702
r_lrange_other	13.975
r_dihedral_angle_3_deg	12.58
r_dihedral_angle_1_deg	7.609
r_scangle_it	7.044
r_scangle_other	7.042
r_mcangle_other	6.307
r_mcangle_it	6.305

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.21
r_dihedral_angle_2_deg	16.615
r_dihedral_angle_6_deg	14.702
r_lrange_other	13.975
r_dihedral_angle_3_deg	12.58
r_dihedral_angle_1_deg	7.609
r_scangle_it	7.044
r_scangle_other	7.042
r_mcangle_other	6.307
r_mcangle_it	6.305
r_scbond_it	4.594
r_scbond_other	4.592
r_rigid_bond_restr	4.134
r_mcbond_it	4.087
r_mcbond_other	4.013
r_dihedral_angle_other_3_deg	2.02
r_angle_refined_deg	1.522
r_angle_other_deg	0.531
r_nbd_refined	0.227
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.182
r_nbd_other	0.179
r_xyhbond_nbd_refined	0.154
r_symmetry_nbd_refined	0.112
r_symmetry_xyhbond_nbd_other	0.1
r_symmetry_xyhbond_nbd_refined	0.095
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2322
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	45

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.

23LX | pdb_000023lx