Experiment: 9HXT

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4AUM

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M of each amino acid, 0.1 M MES/imidazole pH 6.5 Aminoacids: sodium L-glutamate, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine HCl, 0.2 M DL-serine.

Crystal Properties
Matthews coefficient	Solvent content
2.67	50.37

Symmetry
Space Group	P 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 EIGER X 16M		2023-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.6	82.944	91.3	0.061	0.086	0.061	0.995	7	3		577755

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	1.6	1.63			0.729	1.032	0.729	0.549		3.7

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	1.6	82.944	577036	29038	91.452	0.201	0.1994	0.1973	0.2364	0.2342	RANDOM	20.197

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]
-0.872	0.206	0.507	0.702	0.097	0.123

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.322
r_dihedral_angle_3_deg	13.72
r_dihedral_angle_2_deg	13.086
r_dihedral_angle_1_deg	7.186
r_lrange_it	3.528
r_lrange_other	3.528
r_scangle_it	2.423
r_scangle_other	2.423
r_angle_refined_deg	1.939
r_scbond_it	1.649

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.322
r_dihedral_angle_3_deg	13.72
r_dihedral_angle_2_deg	13.086
r_dihedral_angle_1_deg	7.186
r_lrange_it	3.528
r_lrange_other	3.528
r_scangle_it	2.423
r_scangle_other	2.423
r_angle_refined_deg	1.939
r_scbond_it	1.649
r_scbond_other	1.649
r_mcangle_it	1.446
r_mcangle_other	1.446
r_mcbond_it	1.047
r_mcbond_other	1.047
r_angle_other_deg	0.706
r_symmetry_nbd_refined	0.316
r_nbd_other	0.255
r_nbd_refined	0.23
r_symmetry_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.181
r_symmetry_xyhbond_nbd_other	0.127
r_chiral_restr	0.11
r_symmetry_nbtor_other	0.084
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32589
Nucleic Acid Atoms
Solvent Atoms	5122
Heterogen Atoms	725

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.

9HXT | pdb_00009hxt