7RF5 | pdb_00007rf5

X-RAY DIFFRACTION

Serial Crystallography (SX)

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.5	298	0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.19

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	298	CCD	RAYONIX MX340-HS		2018-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.30219	SLAC LCLS	MFX

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	Drop-on-Tape	injection

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	40 (fs)	20	3	9520 (KeV)

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

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	Acoustic Droplet Ejection	4 (µl/min)	undefined (µm)	Acoustic Wave

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	2.23	33.7	99.6	0.965	8	48.1		386505			39.13

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	2.23	2.27	97.52		0.056	0.5

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6DHE	2.23	33.7	1.33	386314	3432	99.63	0.1763	0.1758	0.1766	0.233	0.234	45.97

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.0008
f_angle_d	1.4551
f_chiral_restr	0.0595
f_bond_d	0.0141
f_plane_restr	0.0103

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	41525
Nucleic Acid Atoms
Solvent Atoms	1409
Heterogen Atoms	8627

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.