Experiment: 23LZ

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 Tris pH 8.5, 3.0 M Sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.43

Symmetry
Space Group	P 21 21 2

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	1.9	93.01	99.9	0.213	0.998	13.9	12.5		115699

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	1.9	1.93			1.22	0.462	2.2

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	1.97	73.604	103818	5227	99.83	0.207	0.2051	0.2038	0.2468	0.2543	29.573

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]
3.519			-8.087		4.568

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.25
r_lrange_other	19.858
r_lrange_it	19.856
r_dihedral_angle_6_deg	14.718
r_dihedral_angle_3_deg	13.271
r_scangle_it	11.258
r_scangle_other	11.257
r_mcangle_it	10.785
r_mcangle_other	10.785
r_rigid_bond_restr	8.394

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.25
r_lrange_other	19.858
r_lrange_it	19.856
r_dihedral_angle_6_deg	14.718
r_dihedral_angle_3_deg	13.271
r_scangle_it	11.258
r_scangle_other	11.257
r_mcangle_it	10.785
r_mcangle_other	10.785
r_rigid_bond_restr	8.394
r_scbond_other	7.89
r_scbond_it	7.889
r_mcbond_it	7.389
r_mcbond_other	7.387
r_dihedral_angle_1_deg	6.954
r_dihedral_angle_other_3_deg	2.995
r_angle_refined_deg	1.543
r_angle_other_deg	0.542
r_symmetry_xyhbond_nbd_refined	0.273
r_symmetry_nbd_refined	0.254
r_nbd_other	0.246
r_nbd_refined	0.216
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.143
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.083
r_ncsr_local_group_4	0.082
r_chiral_restr	0.077
r_ncsr_local_group_1	0.076
r_ncsr_local_group_5	0.075
r_ncsr_local_group_3	0.073
r_ncsr_local_group_6	0.071
r_ncsr_local_group_2	0.066
r_xyhbond_nbd_other	0.026
r_bond_refined_d	0.008
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	9476
Nucleic Acid Atoms
Solvent Atoms	311
Heterogen Atoms	264

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.

23LZ | pdb_000023lz