Experiment: 9V63

X-RAY DIFFRACTION

Serial Crystallography (SX)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EW4

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	277	4 M NaCl, 0.1 M citric acid, pH:4

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.49

Symmetry
Space Group	P 32 2 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS EIGER2 R 4M		2024-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976	PETRA III, EMBL c/o DESY	P14 (MX2)

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

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	39.14	98.87	0.36	1.99	10.5		13634

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.83			0.06

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	1EW4	1.7	39.14	13633	649	98.984	0.262	0.2596	0.2602	0.3129	0.3137	14.032

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]
-0.141	-0.07		-0.141		0.456

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.61
r_dihedral_angle_6_deg	16.348
r_dihedral_angle_2_deg	13.656
r_dihedral_angle_1_deg	6.989
r_lrange_it	4.892
r_lrange_other	4.888
r_scangle_it	2.699
r_scangle_other	2.697
r_mcangle_it	2.627
r_mcangle_other	2.625

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.61
r_dihedral_angle_6_deg	16.348
r_dihedral_angle_2_deg	13.656
r_dihedral_angle_1_deg	6.989
r_lrange_it	4.892
r_lrange_other	4.888
r_scangle_it	2.699
r_scangle_other	2.697
r_mcangle_it	2.627
r_mcangle_other	2.625
r_angle_refined_deg	2.276
r_mcbond_it	1.672
r_mcbond_other	1.664
r_scbond_it	1.649
r_scbond_other	1.647
r_angle_other_deg	0.913
r_xyhbond_nbd_refined	0.3
r_symmetry_xyhbond_nbd_refined	0.263
r_nbd_refined	0.198
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.175
r_nbd_other	0.164
r_symmetry_nbd_refined	0.15
r_chiral_restr	0.112
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.044
r_bond_refined_d	0.013
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	863
Nucleic Acid Atoms
Solvent Atoms	43
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.

9V63 | pdb_00009v63