31DG | pdb_000031dg

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, SITTING DROP	6.4	298	PEG 3350 10%, 0.1 M MES pH=6.4

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.53

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		2025-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87313	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	2.04	71.43	99.5	0.064	0.998	17.9	5.5		83270

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	2.04	2.09			0.448	0.904

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	2.04	71.425	14987	734	99.429	0.183	0.1808	0.1902	0.2265	0.2297	RANDOM	28.821

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]
-0.586	-0.293		-0.586		1.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.24
r_dihedral_angle_3_deg	13.551
r_dihedral_angle_2_deg	12.58
r_dihedral_angle_1_deg	6.435
r_lrange_it	5.641
r_lrange_other	5.563
r_scangle_it	3.839
r_scangle_other	3.838
r_mcangle_it	2.673
r_mcangle_other	2.673

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.24
r_dihedral_angle_3_deg	13.551
r_dihedral_angle_2_deg	12.58
r_dihedral_angle_1_deg	6.435
r_lrange_it	5.641
r_lrange_other	5.563
r_scangle_it	3.839
r_scangle_other	3.838
r_mcangle_it	2.673
r_mcangle_other	2.673
r_scbond_it	2.307
r_scbond_other	2.306
r_mcbond_it	1.739
r_mcbond_other	1.739
r_angle_refined_deg	1.432
r_angle_other_deg	0.542
r_symmetry_xyhbond_nbd_other	0.444
r_symmetry_nbd_other	0.209
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.185
r_nbd_other	0.18
r_symmetry_nbd_refined	0.112
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.072
r_bond_refined_d	0.048
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1705
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	73

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.