Experiment: 30TM

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.095 M HEPES pH=7.1-7.7 0.19 M CaCl2 5% glycerol 24-29% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.11

Symmetry
Space Group	C 2 2 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 EIGER2 X 9M		2024-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873128	ESRF	ID23-2

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.8	66.38	89.9	0.997	15.9	12.7		24591

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84			0.943	4.3

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	1.8	66.379	24572	1238	89.876	0.177	0.1748	0.1893	0.2093	0.222	RANDOM	24.519

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]
0.668			-0.457		-0.211

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.501
r_dihedral_angle_3_deg	15.069
r_lrange_other	10.178
r_lrange_it	10.137
r_dihedral_angle_1_deg	9.871
r_scangle_it	8.748
r_scangle_other	8.745
r_mcangle_it	6.477
r_mcangle_other	6.474
r_scbond_it	6.386

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.501
r_dihedral_angle_3_deg	15.069
r_lrange_other	10.178
r_lrange_it	10.137
r_dihedral_angle_1_deg	9.871
r_scangle_it	8.748
r_scangle_other	8.745
r_mcangle_it	6.477
r_mcangle_other	6.474
r_scbond_it	6.386
r_scbond_other	6.385
r_mcbond_it	5.041
r_mcbond_other	5.041
r_dihedral_angle_2_deg	2.538
r_angle_refined_deg	1.587
r_dihedral_angle_other_2_deg	1.173
r_angle_other_deg	0.582
r_nbd_refined	0.227
r_symmetry_xyhbond_nbd_refined	0.207
r_nbd_other	0.201
r_xyhbond_nbd_refined	0.188
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.171
r_metal_ion_refined	0.114
r_symmetry_metal_ion_refined	0.114
r_chiral_restr	0.075
r_symmetry_nbtor_other	0.071
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1887
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	47

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.

30TM | pdb_000030tm