Experiment: 9RGS

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DUB

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	100mM Tris, pH 7.5, 2.1M (NH4)2SO4, 5%v/v octanol

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.4

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 X 9M		2024-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.96863	ESRF	ID30B

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.68	124.7	55.8	0.063	0.989	6.1	4		113963

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	1.68	1.89			0.79	1.6

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	1.68	124.7	113963	5600	55.849	0.211	0.2093	0.2092	0.2418	0.2419	29.78

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]
-0.107			0.333		-0.226

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.422
r_dihedral_angle_3_deg	13.799
r_dihedral_angle_4_deg	12.124
r_dihedral_angle_1_deg	5.732
r_lrange_it	5.019
r_scangle_it	1.818
r_mcangle_it	1.611
r_scbond_it	1.044
r_mcbond_it	0.896
r_angle_refined_deg	0.792

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.422
r_dihedral_angle_3_deg	13.799
r_dihedral_angle_4_deg	12.124
r_dihedral_angle_1_deg	5.732
r_lrange_it	5.019
r_scangle_it	1.818
r_mcangle_it	1.611
r_scbond_it	1.044
r_mcbond_it	0.896
r_angle_refined_deg	0.792
r_nbtor_refined	0.299
r_nbd_refined	0.174
r_symmetry_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.129
r_xyhbond_nbd_refined	0.109
r_chiral_restr	0.063
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11651
Nucleic Acid Atoms
Solvent Atoms	899
Heterogen Atoms	280

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.

9RGS | pdb_00009rgs