9HKJ | pdb_00009hkj

Structure of Formosin D

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	2 uL well (15% PEG8000, 0.1 M MES pH 6.5, 0.2 M NaOAc) + 2 uL protein (1 mg/mL protein in 200 mM NaCl 100 mM TRIS pH 7.5), Cryo: well + 10% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.13	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 21.02	α = 90
b = 41.803	β = 96.609
c = 46.758	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	mirror	2024-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9184	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.7	46.5	98.3	0.199	0.215	0.081	0.994	8.5	6.9	60325	8801		-3	20.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	97.8		1.225	1.32	0.668	0.648	1.8	7	3262

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	1.7	46.447	8790	427	97.993	0.157	0.1549	0.1527	0.2021	0.2011	13.629

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]
0.381		-0.09	0.013		-0.363

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.029
r_dihedral_angle_3_deg	10.595
r_dihedral_angle_1_deg	9.04
r_dihedral_angle_2_deg	6.444
r_lrange_it	4.716
r_lrange_other	4.109
r_scangle_it	2.123
r_scangle_other	2.121
r_angle_refined_deg	1.448
r_scbond_it	1.36
r_scbond_other	1.314
r_mcangle_it	1.183
r_mcangle_other	1.183
r_mcbond_it	0.756
r_mcbond_other	0.718
r_angle_other_deg	0.479
r_nbd_other	0.239
r_nbtor_refined	0.188
r_symmetry_nbd_other	0.181
r_nbd_refined	0.175
r_xyhbond_nbd_refined	0.154
r_symmetry_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.153
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.067
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	682
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing