9RD4 | pdb_00009rd4

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.1 M MgCl2, 0.1 M Hepes-NaOH pH 7.0, 21 % PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.66

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 XE 16M		2022-09-23	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)	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	1.71	29.9	96.7	0.999	17.7	11.9		124894

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	1.71	1.74			0.779

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	1.71	29.9	118171	6343	96.37	0.18469	0.18325	0.193	0.2116	0.2216	RANDOM	16.332

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]
-0.19			-0.86		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.761
r_dihedral_angle_2_deg	8.162
r_dihedral_angle_1_deg	6.643
r_long_range_B_refined	4.123
r_long_range_B_other	4.026
r_scangle_other	3.334
r_scbond_it	2.274
r_scbond_other	2.273
r_mcangle_other	1.928
r_mcangle_it	1.927

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.761
r_dihedral_angle_2_deg	8.162
r_dihedral_angle_1_deg	6.643
r_long_range_B_refined	4.123
r_long_range_B_other	4.026
r_scangle_other	3.334
r_scbond_it	2.274
r_scbond_other	2.273
r_mcangle_other	1.928
r_mcangle_it	1.927
r_angle_refined_deg	1.615
r_mcbond_it	1.437
r_mcbond_other	1.435
r_angle_other_deg	0.858
r_chiral_restr	0.111
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	8607
Nucleic Acid Atoms
Solvent Atoms	636
Heterogen Atoms	31

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.