Experiment: 23MJ

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	0.1M Ammonium citrate pH 6.5, 14% w/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.91

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		2024-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97907	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	48.008	97.1	0.068	0.999	14.4	6.6		57439

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			0.831	0.76	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	1.7	48.008	57409	2856	96.965	0.163	0.1614	0.1725	0.1995	0.2116	27.25

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]
-0.881		0.878	1.532		-0.953

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.161
r_dihedral_angle_6_deg	14.193
r_dihedral_angle_3_deg	12.1
r_lrange_it	7.215
r_lrange_other	7.214
r_dihedral_angle_1_deg	6.929
r_scangle_it	5.597
r_scangle_other	5.597
r_scbond_it	3.741
r_scbond_other	3.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.161
r_dihedral_angle_6_deg	14.193
r_dihedral_angle_3_deg	12.1
r_lrange_it	7.215
r_lrange_other	7.214
r_dihedral_angle_1_deg	6.929
r_scangle_it	5.597
r_scangle_other	5.597
r_scbond_it	3.741
r_scbond_other	3.74
r_mcangle_it	3.546
r_mcangle_other	3.546
r_mcbond_it	2.494
r_mcbond_other	2.494
r_dihedral_angle_other_3_deg	1.992
r_angle_refined_deg	1.62
r_angle_other_deg	0.552
r_symmetry_nbd_refined	0.254
r_nbd_refined	0.216
r_nbd_other	0.212
r_symmetry_xyhbond_nbd_refined	0.207
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.144
r_ncsr_local_group_1	0.088
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.081
r_symmetry_xyhbond_nbd_other	0.042
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	4810
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	132

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.

23MJ | pdb_000023mj