Experiment: 23LW

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	20% v/v Tacsimate pH 7.0, 0.1 M HEPES pH 7.5, 2% v/v Polyethylene glycol 200. Protein concentration 8 mg/ml.

Crystal Properties
Matthews coefficient	Solvent content
2	38.51

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 PILATUS3 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	1.65	106	98.3	0.068	0.994	10.5	6.1		62740

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	1.65	1.68			0.71	0.786	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.65	53.047	62647	3076	98.104	0.195	0.1931	0.2016	0.2384	0.2397	23.032

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]
-0.471		1.027	-0.2		0.177

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.833
r_dihedral_angle_6_deg	14.378
r_dihedral_angle_3_deg	11.675
r_dihedral_angle_1_deg	7.394
r_lrange_it	5.68
r_lrange_other	5.628
r_scangle_it	4.145
r_scangle_other	4.145
r_dihedral_angle_other_3_deg	3.42
r_mcangle_it	3.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.833
r_dihedral_angle_6_deg	14.378
r_dihedral_angle_3_deg	11.675
r_dihedral_angle_1_deg	7.394
r_lrange_it	5.68
r_lrange_other	5.628
r_scangle_it	4.145
r_scangle_other	4.145
r_dihedral_angle_other_3_deg	3.42
r_mcangle_it	3.028
r_mcangle_other	3.028
r_scbond_it	2.778
r_scbond_other	2.777
r_mcbond_it	2.058
r_mcbond_other	2.056
r_angle_refined_deg	1.744
r_angle_other_deg	0.59
r_nbd_refined	0.214
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.186
r_nbd_other	0.171
r_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.129
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.085
r_symmetry_xyhbond_nbd_refined	0.083
r_symmetry_xyhbond_nbd_other	0.064
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4707
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	90

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.

23LW | pdb_000023lw