Experiment: 9HVV

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QCD

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	100 mM Tris/HCl pH 7.8, 1.8 - 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.44

Symmetry
Space Group	C 2 2 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		2019-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976	PETRA III, EMBL c/o DESY	P14 (MX2)

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	1.12	42.53	97.02	0.999	12.34	5.9		104066

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	1.12	1.162			0.797

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	1.12	42.53	98954	5111	97.05	0.12413	0.12301	0.1238	0.14619	0.1461	RANDOM	15.372

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]
1.06			-0.37		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.146
r_dihedral_angle_4_deg	14.369
r_dihedral_angle_3_deg	12.716
r_dihedral_angle_1_deg	6.749
r_scangle_other	3.131
r_long_range_B_refined	3.039
r_rigid_bond_restr	2.928
r_long_range_B_other	2.835
r_scbond_it	2.578
r_scbond_other	2.522

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.146
r_dihedral_angle_4_deg	14.369
r_dihedral_angle_3_deg	12.716
r_dihedral_angle_1_deg	6.749
r_scangle_other	3.131
r_long_range_B_refined	3.039
r_rigid_bond_restr	2.928
r_long_range_B_other	2.835
r_scbond_it	2.578
r_scbond_other	2.522
r_angle_refined_deg	1.975
r_angle_other_deg	1.653
r_mcangle_other	1.505
r_mcangle_it	1.492
r_mcbond_it	1.399
r_mcbond_other	1.344
r_chiral_restr	0.113
r_gen_planes_refined	0.017
r_bond_refined_d	0.013
r_gen_planes_other	0.007
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1966
Nucleic Acid Atoms
Solvent Atoms	306
Heterogen Atoms	43

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.

9HVV | pdb_00009hvv