Experiment: 23MH

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 Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2	38.44

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	1.95	47.27	90.5	0.093	0.998	14.5	6.2		35017

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	1.95	2			0.701	0.6	2.7

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	1.95	47.16	34951	1780	90.373	0.178	0.175	0.1815	0.2286	0.2325	31.044

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]
-0.082		0.869	-0.748		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.883
r_dihedral_angle_6_deg	14.165
r_dihedral_angle_3_deg	13.897
r_lrange_other	8.733
r_lrange_it	8.727
r_dihedral_angle_1_deg	7.349
r_scangle_it	6.045
r_scangle_other	6.045
r_mcangle_other	4.721
r_mcangle_it	4.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.883
r_dihedral_angle_6_deg	14.165
r_dihedral_angle_3_deg	13.897
r_lrange_other	8.733
r_lrange_it	8.727
r_dihedral_angle_1_deg	7.349
r_scangle_it	6.045
r_scangle_other	6.045
r_mcangle_other	4.721
r_mcangle_it	4.72
r_scbond_it	4.034
r_scbond_other	4.034
r_mcbond_it	3.293
r_mcbond_other	3.291
r_dihedral_angle_other_3_deg	2.019
r_angle_refined_deg	1.674
r_angle_other_deg	0.595
r_symmetry_nbd_refined	0.3
r_nbd_other	0.223
r_nbd_refined	0.22
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.135
r_symmetry_nbtor_other	0.089
r_ncsr_local_group_1	0.088
r_chiral_restr	0.087
r_symmetry_xyhbond_nbd_other	0.057
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	4708
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	120

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.

23MH | pdb_000023mh