Experiment: 8BGM

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		Alphafold model

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2 M sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane pH 6.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.66

Symmetry
Space Group	P 21 21 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 16M		2019-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9762	MAX IV	BioMAX

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.7	77.1	99.9	0.14	0.16	0.06	0.99	8.5	10		50841

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	2.7	2.79	99.1		1.56	0.742	1.2	6.1

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	Alphafold model	2.7	63.367	50701	2545	99.917	0.224	0.2224	0.22	0.2629	0.26	53.008

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]
12.337			-4.639		-7.698

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.002
r_dihedral_angle_3_deg	18.307
r_dihedral_angle_4_deg	14.841
r_lrange_it	6.89
r_dihedral_angle_1_deg	6.576
r_scangle_it	4.773
r_mcangle_it	3.916
r_scbond_it	2.878
r_mcbond_it	2.42
r_angle_refined_deg	1.602

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.002
r_dihedral_angle_3_deg	18.307
r_dihedral_angle_4_deg	14.841
r_lrange_it	6.89
r_dihedral_angle_1_deg	6.576
r_scangle_it	4.773
r_mcangle_it	3.916
r_scbond_it	2.878
r_mcbond_it	2.42
r_angle_refined_deg	1.602
r_nbtor_refined	0.312
r_symmetry_xyhbond_nbd_refined	0.246
r_nbd_refined	0.216
r_symmetry_nbd_refined	0.203
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.103
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9696
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

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.

8BGM | pdb_00008bgm