23MF | pdb_000023mf

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 acetate dihydrate, 20% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.69

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	1.78	53.205	96.6	0.095	0.998	12.5	6.6		49628

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	1.78	1.82			0.692	0.774	2.6

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	1.78	53.204	49593	2457	96.419	0.169	0.1667	0.175	0.205	0.214	26.325

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]
0.341		0.949	0.156		-0.842

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.645
r_dihedral_angle_6_deg	13.457
r_dihedral_angle_3_deg	12.869
r_dihedral_angle_1_deg	6.894
r_lrange_it	6.715
r_lrange_other	6.676
r_scangle_it	4.919
r_scangle_other	4.918
r_mcangle_it	3.914
r_mcangle_other	3.914

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.645
r_dihedral_angle_6_deg	13.457
r_dihedral_angle_3_deg	12.869
r_dihedral_angle_1_deg	6.894
r_lrange_it	6.715
r_lrange_other	6.676
r_scangle_it	4.919
r_scangle_other	4.918
r_mcangle_it	3.914
r_mcangle_other	3.914
r_scbond_it	3.218
r_scbond_other	3.218
r_mcbond_it	2.649
r_mcbond_other	2.648
r_angle_refined_deg	1.621
r_dihedral_angle_other_3_deg	0.579
r_angle_other_deg	0.562
r_nbd_refined	0.213
r_symmetry_nbd_refined	0.206
r_symmetry_nbd_other	0.197
r_symmetry_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.183
r_nbd_other	0.174
r_xyhbond_nbd_refined	0.164
r_ncsr_local_group_1	0.089
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.083
r_symmetry_xyhbond_nbd_other	0.05
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	4704
Nucleic Acid Atoms
Solvent Atoms	341
Heterogen Atoms	102

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.