Experiment: 31DE

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QYT

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.4	294	MES 0.1 M pH=6.4; PEG 3350 12%

Crystal Properties
Matthews coefficient	Solvent content
1.82

Symmetry
Space Group	P 31 2 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 EIGER2 X 9M		2026-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	1	ESRF	ID30B

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	45.7	91.7	0.066	0.998	9.3	3.4		11043

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27	81		0.932	0.94		3.4

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	FREE R-VALUE	2.2	45.669	11036	553	90.637	0.176	0.1731	0.1801	0.2354	0.238	50.023

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]
-0.18	-0.09		-0.18		0.585

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.552
r_dihedral_angle_3_deg	12.164
r_lrange_it	8.933
r_lrange_other	8.932
r_dihedral_angle_1_deg	6.944
r_scangle_it	6.916
r_scangle_other	6.914
r_dihedral_angle_2_deg	5.653
r_mcangle_other	4.953
r_mcangle_it	4.945

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.552
r_dihedral_angle_3_deg	12.164
r_lrange_it	8.933
r_lrange_other	8.932
r_dihedral_angle_1_deg	6.944
r_scangle_it	6.916
r_scangle_other	6.914
r_dihedral_angle_2_deg	5.653
r_mcangle_other	4.953
r_mcangle_it	4.945
r_scbond_it	4.356
r_scbond_other	4.354
r_mcbond_it	3.523
r_mcbond_other	3.514
r_angle_refined_deg	1.356
r_angle_other_deg	0.478
r_symmetry_nbd_other	0.203
r_nbd_refined	0.189
r_nbtor_refined	0.187
r_nbd_other	0.164
r_xyhbond_nbd_refined	0.153
r_symmetry_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.129
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.063
r_symmetry_xyhbond_nbd_other	0.05
r_gen_planes_refined	0.008
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1705
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	63

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.

31DE | pdb_000031de