Experiment: 9TJY

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	293	14% 1-propanol, 10% PEG 5000 MME, 0.1 M MES pH 6.8

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.96

Symmetry
Space Group	P 21 21 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 PILATUS 6M-F	Compound refractive element	2022-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.96546	ESRF	MASSIF-1

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	1.77	48.73	93	0.115	0.12	0.033	0.997	12.1	12.9		18728

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	1.77	1.97	64		1.74	1.82	0.52	0.68	1.7	11.5

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	THROUGHOUT	1.774	48.73	18728	974	67.532	0.159	0.156	0.1683	0.2122	0.2222	35.207

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]
5.728			-2.024		-3.704

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.203
r_lrange_other	18.2
r_dihedral_angle_6_deg	15.019
r_scangle_it	13.113
r_scangle_other	13.108
r_mcangle_other	12.353
r_mcangle_it	12.348
r_dihedral_angle_3_deg	11.883
r_scbond_it	8.827
r_scbond_other	8.821

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.203
r_lrange_other	18.2
r_dihedral_angle_6_deg	15.019
r_scangle_it	13.113
r_scangle_other	13.108
r_mcangle_other	12.353
r_mcangle_it	12.348
r_dihedral_angle_3_deg	11.883
r_scbond_it	8.827
r_scbond_other	8.821
r_mcbond_it	8.253
r_mcbond_other	8.226
r_dihedral_angle_1_deg	6.708
r_dihedral_angle_2_deg	6.304
r_rigid_bond_restr	3.813
r_angle_refined_deg	1.472
r_angle_other_deg	0.491
r_chiral_restr_other	0.331
r_nbd_refined	0.205
r_symmetry_nbd_other	0.201
r_nbd_other	0.189
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.084
r_symmetry_nbtor_other	0.083
r_symmetry_nbd_refined	0.08
r_chiral_restr	0.07
r_dihedral_angle_other_2_deg	0.055
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	1517
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	38

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.

9TJY | pdb_00009tjy