Experiment: 9THV

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7AN1

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	40% MPD, 5% PEG 8000, 100 mM Sodium Cacodylate pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.06

Symmetry
Space Group	P 21 21 21

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 EIGER2 XE 16M		2025-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	66.81	100	0.108	0.116	0.044	0.999	10	13.6		75194

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.73	100		2.081	2.242	0.832	0.658	0.4	14.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.7	66.81	75119	3869	100	0.155	0.1528	0.1405	0.1943	0.1825	RANDOM	32.248

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]
0.269			0.423		-0.693

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.515
r_dihedral_angle_6_deg	15.311
r_lrange_other	15.165
r_dihedral_angle_3_deg	12.295
r_scangle_it	12.232
r_scangle_other	12.23
r_mcangle_other	9.099
r_mcangle_it	9.098
r_scbond_it	8.636
r_scbond_other	8.634

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.515
r_dihedral_angle_6_deg	15.311
r_lrange_other	15.165
r_dihedral_angle_3_deg	12.295
r_scangle_it	12.232
r_scangle_other	12.23
r_mcangle_other	9.099
r_mcangle_it	9.098
r_scbond_it	8.636
r_scbond_other	8.634
r_dihedral_angle_1_deg	7.036
r_mcbond_it	6.555
r_mcbond_other	6.548
r_dihedral_angle_2_deg	6.177
r_rigid_bond_restr	3.684
r_angle_refined_deg	1.638
r_angle_other_deg	0.573
r_nbd_other	0.243
r_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.203
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.183
r_symmetry_nbd_refined	0.158
r_xyhbond_nbd_refined	0.144
r_metal_ion_refined	0.103
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.08
r_bond_refined_d	0.008
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	3862
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	14

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.

9THV | pdb_00009thv