8S2W

SSX structure of Arabidopsis thaliana Pdx1.3 grown in seeded batch conditions

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.9	α = 90
b = 177.9	β = 90
c = 117.3	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	Total Frames
1	19325	20268	245400

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	93.33	100	0.96	4.4	47.4		47878			49.36

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		0.17	0.5	45.18

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.5	64.472	47873	2316	99.994	0.169	0.1676	0.1934	RANDOM	59.434

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]
-0.005	-0.002		-0.005		0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.18
r_dihedral_angle_6_deg	14.129
r_lrange_other	11.013
r_lrange_it	11.006
r_scangle_it	9.179
r_scangle_other	9.099
r_dihedral_angle_2_deg	7.892
r_mcangle_it	6.57
r_mcangle_other	6.57
r_dihedral_angle_1_deg	6.304
r_scbond_it	5.847
r_scbond_other	5.714
r_mcbond_it	4.34
r_mcbond_other	4.339
r_angle_refined_deg	1.407
r_angle_other_deg	0.458
r_nbd_refined	0.213
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.157
r_nbd_other	0.152
r_symmetry_xyhbond_nbd_refined	0.141
r_xyhbond_nbd_refined	0.135
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_5	0.07
r_ncsr_local_group_6	0.07
r_ncsr_local_group_3	0.064
r_chiral_restr	0.062
r_ncsr_local_group_1	0.062
r_ncsr_local_group_2	0.061
r_ncsr_local_group_4	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8056
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	20

Software

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