Experiment: 30TO

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
2.61	52.8

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 EIGER X 4M		2024-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.967697	ESRF	MASSIF-3

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	45.57	99.1	0.998	16.7	14.8		26916

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			0.883	3.6

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	45.569	26900	1344	99.028	0.173	0.1716	0.1836	0.2093	0.2149	RANDOM	20.829

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]
1.237			-0.627		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.414
r_dihedral_angle_3_deg	13.354
r_lrange_it	7.006
r_lrange_other	6.879
r_scangle_it	5.626
r_scangle_other	5.624
r_dihedral_angle_1_deg	5.15
r_mcangle_it	3.707
r_mcangle_other	3.706
r_scbond_it	3.675

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.414
r_dihedral_angle_3_deg	13.354
r_lrange_it	7.006
r_lrange_other	6.879
r_scangle_it	5.626
r_scangle_other	5.624
r_dihedral_angle_1_deg	5.15
r_mcangle_it	3.707
r_mcangle_other	3.706
r_scbond_it	3.675
r_scbond_other	3.667
r_mcbond_it	2.54
r_mcbond_other	2.538
r_dihedral_angle_2_deg	2.034
r_angle_refined_deg	1.124
r_dihedral_angle_other_2_deg	0.896
r_angle_other_deg	0.458
r_nbd_refined	0.226
r_symmetry_nbd_refined	0.22
r_nbtor_refined	0.173
r_symmetry_nbd_other	0.166
r_nbd_other	0.156
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.138
r_symmetry_nbtor_other	0.067
r_metal_ion_refined	0.065
r_symmetry_metal_ion_refined	0.063
r_chiral_restr	0.052
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1927
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	49

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.

30TO | pdb_000030to