23MB | pdb_000023mb

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	0.2 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.42

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	2.5	53.28	98.8	0.148	0.995	10.9	6		18373

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	2.5	2.6			0.932	0.39	1.7

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	2.5	53.277	18321	905	98.601	0.181	0.1776	0.1843	0.2463	0.2446	49.572

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]
0.332		1.573	-1.296		0.214

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.635
r_dihedral_angle_3_deg	15.051
r_dihedral_angle_6_deg	13.903
r_lrange_other	10.83
r_lrange_it	10.828
r_dihedral_angle_1_deg	7.685
r_mcangle_it	6.594
r_mcangle_other	6.594
r_scangle_it	6.252
r_scangle_other	6.251

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.635
r_dihedral_angle_3_deg	15.051
r_dihedral_angle_6_deg	13.903
r_lrange_other	10.83
r_lrange_it	10.828
r_dihedral_angle_1_deg	7.685
r_mcangle_it	6.594
r_mcangle_other	6.594
r_scangle_it	6.252
r_scangle_other	6.251
r_mcbond_it	4.148
r_mcbond_other	4.143
r_scbond_it	3.982
r_scbond_other	3.981
r_angle_refined_deg	1.397
r_angle_other_deg	0.481
r_nbd_refined	0.215
r_symmetry_nbd_other	0.201
r_nbd_other	0.185
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.165
r_xyhbond_nbd_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.118
r_dihedral_angle_other_3_deg	0.106
r_ncsr_local_group_1	0.105
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.023
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4630
Nucleic Acid Atoms
Solvent Atoms	101
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.