8C4Y | pdb_00008c4y

X-RAY DIFFRACTION

Serial Crystallography (SX)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VP1

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		294	Purified protein, diluted crystal seeds, and crystallisation buffer were mixed at a 1:1.5:1.5 ratio. Crystallisation buffer was 25% PEG 3350, 200 mM sodium thiocyanate. Crystal seed stock was diluted 1:20 in 25% PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.27

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	298	CCD	MPCCD		2019-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.127	SACLA	BL2

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

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	Silicon nitride chip				25600 apertures

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	10 (fs)	30		undefined (KeV)

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	1.6	30.1	99.8	0.99	0.053	12.1	618.7		37266			12.09

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.628	100		0.91	0.089	4.6	274.5

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	FREE R-VALUE	1.6	30.096	37266	1919	99.791	0.191	0.1903	0.2	0.208	0.2203	17.084

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]
-0.025		-0.503	0.143		0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.941
r_dihedral_angle_3_deg	14.497
r_dihedral_angle_4_deg	13.316
r_dihedral_angle_1_deg	6.147
r_lrange_it	5.386
r_lrange_other	5.382
r_scangle_it	4.497
r_scangle_other	4.496
r_scbond_it	2.861
r_scbond_other	2.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.941
r_dihedral_angle_3_deg	14.497
r_dihedral_angle_4_deg	13.316
r_dihedral_angle_1_deg	6.147
r_lrange_it	5.386
r_lrange_other	5.382
r_scangle_it	4.497
r_scangle_other	4.496
r_scbond_it	2.861
r_scbond_other	2.86
r_mcangle_it	2.605
r_mcangle_other	2.604
r_angle_refined_deg	1.76
r_mcbond_it	1.758
r_mcbond_other	1.753
r_angle_other_deg	1.461
r_symmetry_nbd_refined	0.236
r_symmetry_xyhbond_nbd_refined	0.235
r_nbd_other	0.233
r_nbd_refined	0.205
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.138
r_metal_ion_refined	0.116
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2457
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	1

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.