9RHV | pdb_00009rhv

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	20% PEG3350, 0.2M KSCN

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.29

Symmetry
Space Group	P 41 2 2

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		2024-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

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	2.02	57.05	100	0.11	0.116	0.037	0.999	14.2	17.8		34175

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)
	2.02	2.07	99.6		3.949	4.177	1.354	0.309	0.7	18.1

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.02	54.592	34111	1705	99.962	0.203	0.2014	0.2345	RANDOM	65.249

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]
0.605			0.605		-1.211

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.204
r_dihedral_angle_3_deg	12.561
r_dihedral_angle_2_deg	10.025
r_dihedral_angle_1_deg	8.629
r_lrange_it	6.736
r_lrange_other	6.736
r_scangle_it	5.476
r_scangle_other	5.475
r_scbond_it	3.787
r_scbond_other	3.787

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.204
r_dihedral_angle_3_deg	12.561
r_dihedral_angle_2_deg	10.025
r_dihedral_angle_1_deg	8.629
r_lrange_it	6.736
r_lrange_other	6.736
r_scangle_it	5.476
r_scangle_other	5.475
r_scbond_it	3.787
r_scbond_other	3.787
r_mcangle_it	3.71
r_mcangle_other	3.71
r_mcbond_it	2.709
r_mcbond_other	2.707
r_angle_refined_deg	1.948
r_angle_other_deg	0.967
r_nbd_refined	0.161
r_nbtor_refined	0.153
r_symmetry_nbd_other	0.126
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.107
r_nbd_other	0.089
r_symmetry_nbd_refined	0.076
r_symmetry_xyhbond_nbd_refined	0.074
r_symmetry_nbtor_other	0.065
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_gen_planes_other	0.005
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3104
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	27

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.