9HVT | pdb_00009hvt

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, 1.6 - 1.8 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 5mg/mL OMPD

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.43

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		2019-04-03	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)	Rrim 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	1.3	64.61	99.74	0.09297	0.998	11.21	6.5		69057

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	1.3	1.346			0.433

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	1.3	64.61	65729	3347	99.83	0.14323	0.14172	0.1529	0.17298	0.1784	RANDOM	16.956

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]
0.28			-0.33		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.012
r_dihedral_angle_4_deg	19.498
r_dihedral_angle_3_deg	13.134
r_dihedral_angle_1_deg	6.888
r_long_range_B_refined	3.274
r_long_range_B_other	2.817
r_scangle_other	2.766
r_rigid_bond_restr	2.705
r_scbond_it	2.491
r_scbond_other	2.452

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.012
r_dihedral_angle_4_deg	19.498
r_dihedral_angle_3_deg	13.134
r_dihedral_angle_1_deg	6.888
r_long_range_B_refined	3.274
r_long_range_B_other	2.817
r_scangle_other	2.766
r_rigid_bond_restr	2.705
r_scbond_it	2.491
r_scbond_other	2.452
r_angle_refined_deg	1.824
r_mcangle_other	1.784
r_mcangle_it	1.779
r_angle_other_deg	1.591
r_mcbond_it	1.589
r_mcbond_other	1.576
r_chiral_restr	0.101
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.002
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	1959
Nucleic Acid Atoms
Solvent Atoms	327
Heterogen Atoms	45

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.