Experiment: 7JRI

X-RAY DIFFRACTION

Serial Crystallography (SX)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6PTQ

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	0.17 M Ammonium acetate, 0.085 M Sodium citrate tribasic dihydrate pH 5.6, 25.5% w/v Polyethylene glycol 4000, 15% v/v Glycerol (cryo-screen solution) and 3 % w/v Benzamidine Hydrochloride mixed with 60 mg/mL protein (3:2) protein to mother liquor ratio

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.23

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	293	CCD	MPCCD		2019-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.38	SACLA	BL2

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	Folded in Nuclear Grade Grease	injection

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

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	41817	89389	41817

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	viscous jet extrusion	4 (µl/min)	undefined (µm)	HPLC			nuclear grade grease

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	2.1	25	100	0.994	0.094	7.6	449.4		68919

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	2.1	2.14	100		0.31	1.12		203

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	6PTQ	2.4	24.33	36457	1792	85.53	0.29435	0.29241	0.2938	0.33349	0.3334	RANDOM	22.116

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]
0.8		0.32	-0.57		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.73
r_dihedral_angle_3_deg	28.073
r_dihedral_angle_4_deg	20.299
r_dihedral_angle_1_deg	12.277
r_long_range_B_other	6.118
r_long_range_B_refined	6.115
r_mcangle_it	3.067
r_mcangle_other	3.067
r_scangle_other	2.393
r_angle_refined_deg	2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.73
r_dihedral_angle_3_deg	28.073
r_dihedral_angle_4_deg	20.299
r_dihedral_angle_1_deg	12.277
r_long_range_B_other	6.118
r_long_range_B_refined	6.115
r_mcangle_it	3.067
r_mcangle_other	3.067
r_scangle_other	2.393
r_angle_refined_deg	2.12
r_mcbond_it	1.87
r_mcbond_other	1.868
r_scbond_it	1.419
r_scbond_other	1.419
r_angle_other_deg	1.233
r_chiral_restr	0.21
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7320
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	95

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.

7JRI | pdb_00007jri