31DF | pdb_000031df

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	293	PEG 3350 12%, MES 0.1 M pH=6.4

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.65

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		2025-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

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	1.89	41.505	99.8	0.089	0.999	15	10		19254

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	1.89	1.93			0.901	0.815	2.5	8.8

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	1.89	41.505	19243	973	99.844	0.188	0.1862	0.1977	0.2253	0.2394	RANDOM	29.038

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]
-1.024	-0.512		-1.024		3.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	14.558
r_dihedral_angle_6_deg	13.154
r_dihedral_angle_3_deg	11.724
r_dihedral_angle_1_deg	6.667
r_dihedral_angle_2_deg	6.037
r_lrange_it	5.238
r_lrange_other	5.171
r_scangle_it	3.701
r_scangle_other	3.7
r_mcangle_it	2.564

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	14.558
r_dihedral_angle_6_deg	13.154
r_dihedral_angle_3_deg	11.724
r_dihedral_angle_1_deg	6.667
r_dihedral_angle_2_deg	6.037
r_lrange_it	5.238
r_lrange_other	5.171
r_scangle_it	3.701
r_scangle_other	3.7
r_mcangle_it	2.564
r_mcangle_other	2.563
r_scbond_it	2.219
r_scbond_other	2.218
r_mcbond_it	1.609
r_mcbond_other	1.608
r_angle_refined_deg	1.116
r_angle_other_deg	0.422
r_nbd_refined	0.188
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.131
r_nbd_other	0.115
r_symmetry_xyhbond_nbd_refined	0.11
r_symmetry_nbd_refined	0.107
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.057
r_gen_planes_refined	0.005
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1714
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	60

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.