Experiment: 9RTD

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZH2

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M sodium citrate pH 5.5, 15% PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.44

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 EIGER X 16M		2024-12-15	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)	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	1.95	87.95	92.5	0.347	6.5	13		55431

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.21			1.56

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	2.1	87.949	54446	2730	59.801	0.205	0.2022	0.2091	0.2666	0.2671	21.548

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]
-0.211			-0.139		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.092
r_dihedral_angle_6_deg	14.702
r_dihedral_angle_2_deg	7.423
r_dihedral_angle_1_deg	6.476
r_lrange_it	4.628
r_lrange_other	4.628
r_scangle_it	3.599
r_scangle_other	3.598
r_mcangle_it	2.403
r_mcangle_other	2.403

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.092
r_dihedral_angle_6_deg	14.702
r_dihedral_angle_2_deg	7.423
r_dihedral_angle_1_deg	6.476
r_lrange_it	4.628
r_lrange_other	4.628
r_scangle_it	3.599
r_scangle_other	3.598
r_mcangle_it	2.403
r_mcangle_other	2.403
r_scbond_it	2.225
r_scbond_other	2.225
r_angle_refined_deg	1.679
r_mcbond_it	1.468
r_mcbond_other	1.466
r_angle_other_deg	0.538
r_dihedral_angle_other_2_deg	0.535
r_nbd_refined	0.221
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.175
r_nbd_other	0.156
r_symmetry_xyhbond_nbd_refined	0.147
r_xyhbond_nbd_refined	0.145
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.072
r_xyhbond_nbd_other	0.052
r_symmetry_xyhbond_nbd_other	0.029
r_chiral_restr_other	0.008
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9307
Nucleic Acid Atoms	661
Solvent Atoms	166
Heterogen Atoms

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.

9RTD | pdb_00009rtd