9Y7U | pdb_00009y7u

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ZZX

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	28% PEG 3,350, 0.2M LiSO4, 0.1M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.54

Symmetry
Space Group	P 21 21 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	Horizontal pre-focus bimorph mirror & KB bimorph mirrors	2024-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97931	NSLS-II	17-ID-2

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.65	34.22	94.7	0.032	0.045	0.032	0.999	10.6	1.9		50319

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	96.4		0.691	0.977	0.691	0.538	1.1	1.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.65	34.22	50273	2614	94.498	0.155	0.1513	0.1558	0.2267	0.2283	RANDOM	30.293

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]
-1.11			-0.999		2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.575
r_dihedral_angle_6_deg	16.179
r_dihedral_angle_3_deg	15.122
r_lrange_it	13.244
r_lrange_other	13.023
r_scangle_it	10.212
r_scangle_other	9.889
r_mcangle_other	7.465
r_mcangle_it	7.462
r_scbond_it	7.283

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.575
r_dihedral_angle_6_deg	16.179
r_dihedral_angle_3_deg	15.122
r_lrange_it	13.244
r_lrange_other	13.023
r_scangle_it	10.212
r_scangle_other	9.889
r_mcangle_other	7.465
r_mcangle_it	7.462
r_scbond_it	7.283
r_scbond_other	7.06
r_dihedral_angle_1_deg	6.33
r_rigid_bond_restr	5.668
r_mcbond_it	5.395
r_mcbond_other	5.375
r_dihedral_angle_other_2_deg	5.05
r_angle_refined_deg	2.318
r_angle_other_deg	0.796
r_nbd_refined	0.211
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.183
r_nbd_other	0.17
r_symmetry_xyhbond_nbd_refined	0.134
r_symmetry_nbd_refined	0.127
r_ncsr_local_group_1	0.126
r_chiral_restr	0.119
r_symmetry_nbtor_other	0.092
r_symmetry_xyhbond_nbd_other	0.04
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3264
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	174

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.