Experiment: 8WF5

X-RAY DIFFRACTION

Serial Crystallography (SX)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DWR

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	2.8 M ammonium sulfate, 100 mM Tis-HCl buffer (pH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.79

Symmetry
Space Group	P 1 21 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 PILATUS 6M		2023-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00	SPring-8	BL45XU

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

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	1.72	33.792	96.4	0.155	0.991	10.4	6.5		12813

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	1.72	1.75			0.738	0.681	3.2

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	THROUGHOUT	1.72	33.792	12804	639	95.724	0.16	0.1572	0.1677	0.2155	0.2251	19.474

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]
0.008		0.006	-0.005		-0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.876
r_dihedral_angle_3_deg	13.74
r_lrange_it	6.638
r_lrange_other	6.535
r_dihedral_angle_2_deg	5.934
r_dihedral_angle_1_deg	5.238
r_scangle_it	4.386
r_scangle_other	4.384
r_scbond_it	2.839
r_scbond_other	2.838

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.876
r_dihedral_angle_3_deg	13.74
r_lrange_it	6.638
r_lrange_other	6.535
r_dihedral_angle_2_deg	5.934
r_dihedral_angle_1_deg	5.238
r_scangle_it	4.386
r_scangle_other	4.384
r_scbond_it	2.839
r_scbond_other	2.838
r_mcangle_other	2.799
r_mcangle_it	2.786
r_angle_refined_deg	1.973
r_mcbond_it	1.752
r_mcbond_other	1.739
r_angle_other_deg	0.525
r_xyhbond_nbd_refined	0.224
r_nbd_refined	0.218
r_nbd_other	0.209
r_symmetry_nbd_refined	0.199
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.15
r_chiral_restr	0.071
r_symmetry_nbtor_other	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.008
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1194
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	68

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.

8WF5 | pdb_00008wf5