9SE9 | pdb_00009se9

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Protein concentration: 12 mg/ml. Reservoir buffer: 30% PEG 3350, 0.1M sodium citrate pH 5.9, 0.15M MgCl2, 0.1M bis-tris pH 6.0. Cryoprotectant: 20% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.84

Symmetry
Space Group	P 1 21 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 PILATUS 2M-F		2018-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	SLS	X06DA

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	1.97	63.67	100	0.078	0.085	0.033	0.999	13.1	6.4		77687

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	1.97	2.04			0.919	1	0.393	0.669		6.3

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	1.97	63.67	73826	3842	100	0.19463	0.19281	0.1993	0.22975	0.2334	RANDOM	48.871

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]
0.12		0.51	-1.66		1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.38
r_dihedral_angle_4_deg	20.233
r_dihedral_angle_3_deg	13.613
r_long_range_B_refined	7.353
r_long_range_B_other	7.353
r_dihedral_angle_1_deg	6.482
r_scangle_other	3.55
r_mcangle_it	3.453
r_mcangle_other	3.453
r_scbond_it	2.255

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.38
r_dihedral_angle_4_deg	20.233
r_dihedral_angle_3_deg	13.613
r_long_range_B_refined	7.353
r_long_range_B_other	7.353
r_dihedral_angle_1_deg	6.482
r_scangle_other	3.55
r_mcangle_it	3.453
r_mcangle_other	3.453
r_scbond_it	2.255
r_scbond_other	2.255
r_mcbond_it	2.05
r_mcbond_other	2.05
r_angle_refined_deg	1.345
r_angle_other_deg	0.946
r_chiral_restr	0.074
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	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	8339
Nucleic Acid Atoms
Solvent Atoms	344
Heterogen Atoms	201

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.