7QYD | pdb_00007qyd

mosquitocidal Cry11Ba determined at pH 6.5 from naturally-occurring nanocrystals by Serial femtosecond crystallography

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7QX4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	IN CELL	6.5	303	crystallized in vivo

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 168.245	α = 90
b = 158.528	β = 90
c = 57.534	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	CS-PAD CXI-2		2016-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.304373	SLAC LCLS	CXI

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	microfluidic electrokinetic sample holder	injection

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	50 (fs)	120	1	undefined (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	microfluidic electrokinetic sample holder	undefined (µl/min)	undefined (µm)

Data Collection

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	2.4	42.1	100	0.991	0.0145	4.7	57.9		61141

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	2.4	2.44	100		0.359	0.849		17.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7QX4	2.4	42.1	55060	5991	99.92	0.187	0.1826	0.19	0.2309	0.23	47.7

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]
-1.446			-0.253		1.699

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.531
r_dihedral_angle_3_deg	12.513
r_dihedral_angle_4_deg	11.891
r_lrange_it	7.983
r_lrange_other	7.964
r_scangle_it	6.411
r_scangle_other	6.411
r_dihedral_angle_1_deg	6.112
r_mcangle_it	5.216
r_mcangle_other	5.216
r_scbond_it	4.253
r_scbond_other	4.253
r_mcbond_it	3.494
r_mcbond_other	3.487
r_angle_other_deg	2.266
r_angle_refined_deg	1.324
r_nbd_other	0.223
r_symmetry_nbd_other	0.211
r_nbd_refined	0.179
r_nbtor_refined	0.168
r_symmetry_nbd_refined	0.159
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_other	0.085
r_symmetry_nbtor_other	0.068
r_chiral_restr	0.054
r_bond_other_d	0.035
r_bond_refined_d	0.008
r_gen_planes_other	0.008
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10064
Nucleic Acid Atoms
Solvent Atoms	622
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
cctbx.xfel	data reduction
PHASER	phasing
cctbx.xfel	data scaling