Experiment: 23MC

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	2% v/v TacsimateTM pH 6.0, 0.1 M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.25

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	1.87	53.21	91.9	0.094	0.998	12.8	6.6		40429

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	1.87	1.91			0.952	0.691	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	1.87	52.715	40403	2005	91.756	0.177	0.1744	0.1824	0.2149	0.2199	33.658

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]
1.068		1.871	-1.468		-0.426

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.425
r_dihedral_angle_6_deg	14.256
r_dihedral_angle_3_deg	12.687
r_lrange_it	7.414
r_lrange_other	7.403
r_dihedral_angle_1_deg	7.112
r_scangle_it	5.512
r_scangle_other	5.512
r_mcangle_other	4.029
r_mcangle_it	4.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.425
r_dihedral_angle_6_deg	14.256
r_dihedral_angle_3_deg	12.687
r_lrange_it	7.414
r_lrange_other	7.403
r_dihedral_angle_1_deg	7.112
r_scangle_it	5.512
r_scangle_other	5.512
r_mcangle_other	4.029
r_mcangle_it	4.028
r_scbond_it	3.577
r_scbond_other	3.576
r_mcbond_it	2.775
r_mcbond_other	2.769
r_angle_refined_deg	1.523
r_dihedral_angle_other_3_deg	1.488
r_angle_other_deg	0.518
r_symmetry_xyhbond_nbd_other	0.227
r_symmetry_xyhbond_nbd_refined	0.209
r_nbd_refined	0.207
r_symmetry_nbd_refined	0.205
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.18
r_nbd_other	0.18
r_xyhbond_nbd_refined	0.149
r_symmetry_nbtor_other	0.083
r_ncsr_local_group_1	0.081
r_chiral_restr	0.074
r_bond_refined_d	0.007
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	4696
Nucleic Acid Atoms
Solvent Atoms	257
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.

23MC | pdb_000023mc