Experiment: 6NKN

X-RAY DIFFRACTION

Serial Crystallography (SX)

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.8	277	36 hour crystallization in a cold room with stirring

Crystal Properties
Matthews coefficient	Solvent content
4.4	72.05

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	293	PIXEL	CS-PAD XPP		2016-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.306	SLAC LCLS	MFX

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	40 (fs)	120		9.5 (KeV)

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	98993	108241	98993

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	GDVN	undefined (µl/min)	undefined (µm)

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	2.5	10.5	98.54	0.989	5.1	1038		231448

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	2.5	2.561	100		0.168	0.56

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2dyr	2.5	10.5	231448	12143	98.54	0.17777	0.17565	0.21736	0.2004	RANDOM	63.44

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]
-2.5			0.95		1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.896
r_dihedral_angle_3_deg	17.771
r_dihedral_angle_4_deg	17.572
r_long_range_B_refined	11.656
r_long_range_B_other	11.656
r_scangle_other	8.667
r_mcangle_it	7.367
r_mcangle_other	7.367
r_dihedral_angle_1_deg	7.099
r_scbond_it	5.517

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.896
r_dihedral_angle_3_deg	17.771
r_dihedral_angle_4_deg	17.572
r_long_range_B_refined	11.656
r_long_range_B_other	11.656
r_scangle_other	8.667
r_mcangle_it	7.367
r_mcangle_other	7.367
r_dihedral_angle_1_deg	7.099
r_scbond_it	5.517
r_scbond_other	5.517
r_mcbond_it	4.834
r_mcbond_other	4.829
r_angle_refined_deg	1.696
r_angle_other_deg	1.388
r_chiral_restr	0.155
r_gen_planes_other	0.017
r_gen_planes_refined	0.01
r_bond_refined_d	0.008
r_bond_other_d	0.005
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	28419
Nucleic Acid Atoms
Solvent Atoms	772
Heterogen Atoms	2228

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.

6NKN | pdb_00006nkn