Experiment: 9RDG

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CKQ

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		292	100 mM Tris-HCl pH 8.5, 12% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.6

Symmetry
Space Group	P 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 EIGER2 XE 16M		2023-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	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	1.5	48.44	98	0.071	0.1	0.071	0.991	7.4	3.6		147933

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)
	1.5	1.53	96.7		0.646	0.913	0.646	0.631	1.3	3.7

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	48.44	147844	7296	97.935	0.19	0.189	0.2147	15.224

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]
0.176	-0.047	0.729	0.113	-0.184	-0.403

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.654
r_dihedral_angle_3_deg	10.808
r_dihedral_angle_2_deg	9.333
r_dihedral_angle_1_deg	7.282
r_lrange_it	4.049
r_lrange_other	3.815
r_scangle_it	2.849
r_scangle_other	2.849
r_scbond_it	1.954
r_scbond_other	1.954

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.654
r_dihedral_angle_3_deg	10.808
r_dihedral_angle_2_deg	9.333
r_dihedral_angle_1_deg	7.282
r_lrange_it	4.049
r_lrange_other	3.815
r_scangle_it	2.849
r_scangle_other	2.849
r_scbond_it	1.954
r_scbond_other	1.954
r_angle_refined_deg	1.95
r_mcangle_it	1.835
r_mcangle_other	1.834
r_mcbond_it	1.346
r_mcbond_other	1.344
r_angle_other_deg	0.995
r_chiral_restr	0.238
r_nbd_refined	0.195
r_nbtor_refined	0.162
r_nbd_other	0.155
r_symmetry_nbd_other	0.143
r_xyhbond_nbd_refined	0.108
r_symmetry_nbd_refined	0.107
r_symmetry_xyhbond_nbd_refined	0.098
r_symmetry_nbtor_other	0.064
r_ncsr_local_group_1	0.054
r_bond_refined_d	0.012
r_bond_other_d	0.005
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6252
Nucleic Acid Atoms
Solvent Atoms	897
Heterogen Atoms	64

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.

9RDG | pdb_00009rdg