6YRJ | pdb_00006yrj

X-RAY DIFFRACTION

Serial Crystallography (SX)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		Unpublished

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7.5	291	6-10 mg/mL of protein in 50mM Sodium acetate, 150mM NaCl pH 5 mixed with 150 mM mM MgCl2, 150 mM HEPES, 20% PEG 4000, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.67

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	301	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	chip fixed target	fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	Silicon 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	1.85	103	100	0.976	0.136	5	518		175001			26.9

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	1.85	1.9	100		0.569	0.678		360

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 (Observed)	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X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Unpublished	1.85	13	172358	1982	99.62	0.1597	0.1593	0.1632	0.1916	0.1936	RANDOM	33.503

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]
0.24			-0.15		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.167
r_dihedral_angle_4_deg	17.823
r_dihedral_angle_3_deg	13.507
r_dihedral_angle_1_deg	6.934
r_angle_refined_deg	1.716
r_angle_other_deg	1.447
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.167
r_dihedral_angle_4_deg	17.823
r_dihedral_angle_3_deg	13.507
r_dihedral_angle_1_deg	6.934
r_angle_refined_deg	1.716
r_angle_other_deg	1.447
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13922
Nucleic Acid Atoms
Solvent Atoms	810
Heterogen Atoms	259

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.