Experiment: 9RYZ

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		2024-11-13	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	2.15	225.76	100	0.278	0.054	0.998	9.4	27.7		403283

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	2.15	2.19			4.267	0.469	0.8	28.5

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	2.15	225.76	403252	20057	99.991	0.22	0.2185	0.2284	0.2564	0.2651	47.082

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]
-0.317			-0.317		0.634

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.525
r_dihedral_angle_6_deg	14.42
r_dihedral_angle_2_deg	10.296
r_lrange_other	9.308
r_lrange_it	9.298
r_dihedral_angle_1_deg	7
r_mcangle_it	6.993
r_mcangle_other	6.993
r_scangle_it	6.858
r_scangle_other	6.858

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.525
r_dihedral_angle_6_deg	14.42
r_dihedral_angle_2_deg	10.296
r_lrange_other	9.308
r_lrange_it	9.298
r_dihedral_angle_1_deg	7
r_mcangle_it	6.993
r_mcangle_other	6.993
r_scangle_it	6.858
r_scangle_other	6.858
r_mcbond_it	4.583
r_mcbond_other	4.582
r_scbond_it	4.445
r_scbond_other	4.445
r_dihedral_angle_other_2_deg	2.279
r_angle_refined_deg	1.684
r_angle_other_deg	0.567
r_symmetry_xyhbond_nbd_refined	0.228
r_nbd_refined	0.223
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.156
r_nbd_other	0.147
r_symmetry_nbd_refined	0.133
r_symmetry_xyhbond_nbd_other	0.09
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.078
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32480
Nucleic Acid Atoms
Solvent Atoms	1050
Heterogen Atoms	804

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.

9RYZ | pdb_00009ryz