7IMG | pdb_00007img

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YUN

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	298	0.1 M HEPES, pH 7.8, 10 % isopropanol, 23 % PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.97

Symmetry
Space Group	I 41

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 9M		2020-08-12		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91261	Diamond	I04-1

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.681	44.336	53.6	0.065	0.071	0.028	12.1	6.3		9352

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.681	1.802		14.5	0.826	0.919	0.391		5.2

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	6YUN	1.68	62.7	8893	460	53.57	0.20448	0.20108	0.2511	0.26789	0.2933	RANDOM	29.903

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]
0.13			0.13		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.358
r_dihedral_angle_4_deg	18.345
r_dihedral_angle_3_deg	16.757
r_dihedral_angle_1_deg	6.673
r_long_range_B_refined	4.812
r_long_range_B_other	4.618
r_mcangle_it	3.145
r_mcangle_other	3.144
r_scangle_other	2.227
r_mcbond_other	1.656

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.358
r_dihedral_angle_4_deg	18.345
r_dihedral_angle_3_deg	16.757
r_dihedral_angle_1_deg	6.673
r_long_range_B_refined	4.812
r_long_range_B_other	4.618
r_mcangle_it	3.145
r_mcangle_other	3.144
r_scangle_other	2.227
r_mcbond_other	1.656
r_mcbond_it	1.588
r_angle_refined_deg	1.405
r_angle_other_deg	1.195
r_scbond_it	1.175
r_scbond_other	1.175
r_chiral_restr	0.058
r_gen_planes_refined	0.007
r_bond_refined_d	0.005
r_gen_planes_other	0.003
r_bond_other_d	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	918
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	17

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.