Experiment: 9RZ0

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9I2T

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295.15	4 M ammonium acetate, 0.1 M Bis-Trispropane, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.99	69.17

Symmetry
Space Group	I 4 2 2

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 X 16M		2024-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.953731	Diamond	I04

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.3	225.76	100	0.348	0.067	0.996	7.3	27.5		329974

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34			5.549	0.368

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	FREE R-VALUE	2.3	196.532	329796	16805	99.946	0.2	0.1979	0.2066	0.2425	0.2481	54.02

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]
-0.467			-0.467		0.934

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.424
r_dihedral_angle_6_deg	14.188
r_dihedral_angle_2_deg	12.063
r_lrange_other	10.037
r_lrange_it	10.025
r_mcangle_it	7.526
r_mcangle_other	7.526
r_scangle_it	7.526
r_scangle_other	7.526
r_dihedral_angle_1_deg	7.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.424
r_dihedral_angle_6_deg	14.188
r_dihedral_angle_2_deg	12.063
r_lrange_other	10.037
r_lrange_it	10.025
r_mcangle_it	7.526
r_mcangle_other	7.526
r_scangle_it	7.526
r_scangle_other	7.526
r_dihedral_angle_1_deg	7.136
r_mcbond_it	4.947
r_mcbond_other	4.946
r_scbond_it	4.898
r_scbond_other	4.898
r_dihedral_angle_other_2_deg	3.162
r_angle_refined_deg	1.649
r_angle_other_deg	0.545
r_nbd_refined	0.226
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.17
r_xyhbond_nbd_refined	0.152
r_nbd_other	0.146
r_symmetry_xyhbond_nbd_other	0.126
r_symmetry_nbtor_other	0.082
r_symmetry_nbd_refined	0.078
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32455
Nucleic Acid Atoms
Solvent Atoms	1141
Heterogen Atoms	828

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.

9RZ0 | pdb_00009rz0