8S2X | pdb_00008s2x

SSX structure of Arabidopsis thaliana Pdx1.3 grown in microfluidic droplets

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	7NHF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROFLUIDIC	7	294	600 mM Sodium citrate and 100 mM HEPES pH 7

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.3	α = 90
b = 180.3	β = 90
c = 119.2	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	PSI JUNGFRAU 4M		2023-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.07	ESRF	ID29

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	SOS Chip	fixed target

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	20635	20827	20635

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	2.5	94.75	100	0.96	5	44.2		50011			45.27

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	2.54	100		0.27	0.8	44.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.5	65.396	50003	2510	99.984	0.16	0.1584	0.1671	0.1883	0.1929	59.187

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]
0.006	0.003		0.006		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.633
r_dihedral_angle_6_deg	14.104
r_lrange_it	11.962
r_lrange_other	11.951
r_scangle_it	9.728
r_scangle_other	9.702
r_dihedral_angle_2_deg	9.081
r_mcangle_it	7.523
r_mcangle_other	7.523
r_dihedral_angle_1_deg	6.5
r_scbond_it	6.193
r_scbond_other	6.109
r_mcbond_it	4.956
r_mcbond_other	4.956
r_angle_refined_deg	1.511
r_angle_other_deg	0.504
r_nbd_refined	0.206
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.168
r_nbd_other	0.162
r_symmetry_nbd_refined	0.14
r_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_refined	0.107
r_symmetry_nbtor_other	0.079
r_ncsr_local_group_3	0.078
r_ncsr_local_group_6	0.075
r_chiral_restr	0.072
r_ncsr_local_group_5	0.07
r_ncsr_local_group_2	0.063
r_ncsr_local_group_1	0.06
r_ncsr_local_group_4	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8088
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
MOLREP	phasing