Experiment: 9RY2

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	0.1 M Sodium citrate, pH 5 3.2 M Ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.13

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 EIGER2 XE 16M		2024-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	67.033	99.9	0.27	0.292	0.109	6.2	7		55915			14.61

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.04	97.2		1.253	0.465	1.4	7.2

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	2.001	67.033	55880	1967	99.821	0.205	0.2038	0.2111	0.2443	0.2498	20.877

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]
-0.17		-0.023	0.047		0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.139
r_dihedral_angle_3_deg	13.625
r_dihedral_angle_1_deg	6.168
r_lrange_other	5.583
r_lrange_it	5.582
r_dihedral_angle_2_deg	5.519
r_scangle_it	4.523
r_scangle_other	4.522
r_scbond_it	2.84
r_scbond_other	2.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.139
r_dihedral_angle_3_deg	13.625
r_dihedral_angle_1_deg	6.168
r_lrange_other	5.583
r_lrange_it	5.582
r_dihedral_angle_2_deg	5.519
r_scangle_it	4.523
r_scangle_other	4.522
r_scbond_it	2.84
r_scbond_other	2.83
r_mcangle_it	2.433
r_mcangle_other	2.433
r_mcbond_it	1.701
r_mcbond_other	1.701
r_angle_refined_deg	1.696
r_angle_other_deg	0.586
r_symmetry_nbd_refined	0.292
r_nbd_refined	0.214
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.169
r_xyhbond_nbd_refined	0.163
r_nbd_other	0.161
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.055
r_ncsr_local_group_1	0.052
r_bond_refined_d	0.009
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	6255
Nucleic Acid Atoms
Solvent Atoms	549
Heterogen Atoms	102

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.

9RY2 | pdb_00009ry2