Experiment: 6LPD

X-RAY DIFFRACTION

Serial Crystallography (SX)

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AJO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291.15	0.1 M HEPES pH 7.5, 20% v/v Jeffamine M-600

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.005	α = 90
b = 153.491	β = 90
c = 153.818	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
2	1	x-ray	100	CCD	ADSC QUANTUM 315r		2017-07-11	M	SINGLE WAVELENGTH
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2017-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
2	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.960	SSRF	BL17U1
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.960	SSRF	BL17U1

Serial Crystallography

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

Data Collection

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	1.65	108.65	96.383	0.88	38.3	5.3		215690

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	1.65	1.66			0.88

Refinement

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	3AJO	1.65	108.65	197507	10411	96.38	0.1106	0.1084	0.13	0.1533	0.17	RANDOM	17.279

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]
0.04			-0.05		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.257
r_sphericity_free	36.205
r_dihedral_angle_4_deg	16.024
r_dihedral_angle_3_deg	13.644
r_sphericity_bonded	13.229
r_rigid_bond_restr	5.694
r_dihedral_angle_1_deg	5.595
r_angle_refined_deg	2.53
r_angle_other_deg	1.302
r_chiral_restr	0.176

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.257
r_sphericity_free	36.205
r_dihedral_angle_4_deg	16.024
r_dihedral_angle_3_deg	13.644
r_sphericity_bonded	13.229
r_rigid_bond_restr	5.694
r_dihedral_angle_1_deg	5.595
r_angle_refined_deg	2.53
r_angle_other_deg	1.302
r_chiral_restr	0.176
r_bond_refined_d	0.031
r_gen_planes_refined	0.014
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8355
Nucleic Acid Atoms
Solvent Atoms	1459
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

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.