Experiment: 9RO3

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9G92

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294.15	0.1 M Tris/HCl, 0.1 M KSCN, PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.28

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 PILATUS 6M		2023-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	45.56	98.67	0.999	8.84	6.7		102375

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.279			0.537

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	45.5	97310	5056	98.68	0.206	0.20418	0.2078	0.2414	0.2428	RANDOM	44.449

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]
-0.2		-1.29	0.33		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.518
r_dihedral_angle_4_deg	17.375
r_dihedral_angle_3_deg	14.792
r_long_range_B_other	8.708
r_long_range_B_refined	8.703
r_dihedral_angle_1_deg	7.169
r_scangle_other	7.143
r_mcangle_it	5.738
r_mcangle_other	5.738
r_scbond_it	4.928

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.518
r_dihedral_angle_4_deg	17.375
r_dihedral_angle_3_deg	14.792
r_long_range_B_other	8.708
r_long_range_B_refined	8.703
r_dihedral_angle_1_deg	7.169
r_scangle_other	7.143
r_mcangle_it	5.738
r_mcangle_other	5.738
r_scbond_it	4.928
r_scbond_other	4.928
r_mcbond_it	4.266
r_mcbond_other	4.263
r_angle_refined_deg	1.52
r_angle_other_deg	1.283
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_bond_other_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14886
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	215

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.

9RO3 | pdb_00009ro3