9HZ9 | pdb_00009hz9

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5G0C

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	296	2.5 M ammonium sulfate, 100 mM Tris, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.91

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 6M		2023-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	40.87	100	0.092	0.097	0.998	22.5	17.5		22560

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	99.8		0.152	0.161	0.995	13.7	18.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1.8	40.87	22548	1145	99.938	0.12	0.1161	0.1394	0.1954	0.2059	15.445

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]
0.346		-0.072	-0.172		-0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.592
r_dihedral_angle_3_deg	14.459
r_dihedral_angle_4_deg	13.408
r_dihedral_angle_1_deg	7.161
r_lrange_other	5.275
r_lrange_it	5.187
r_scangle_it	4.71
r_scangle_other	4.708
r_scbond_it	3.798
r_scbond_other	3.796

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.592
r_dihedral_angle_3_deg	14.459
r_dihedral_angle_4_deg	13.408
r_dihedral_angle_1_deg	7.161
r_lrange_other	5.275
r_lrange_it	5.187
r_scangle_it	4.71
r_scangle_other	4.708
r_scbond_it	3.798
r_scbond_other	3.796
r_mcangle_it	3.196
r_mcangle_other	3.114
r_rigid_bond_restr	2.694
r_mcbond_it	2.405
r_mcbond_other	2.404
r_angle_refined_deg	1.823
r_angle_other_deg	1.47
r_symmetry_nbd_refined	0.305
r_nbd_refined	0.242
r_symmetry_xyhbond_nbd_refined	0.207
r_nbd_other	0.203
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.061
r_metal_ion_refined	0.061
r_xyhbond_nbd_other	0.031
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2055
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	33

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.