8KD8 | pdb_00008kd8

N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF N-terminal domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q4QF55-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	0.2M potassium sodium tartrate tetrahydrate, 20% w/v polyethylene glycol 3350, cryoprotected with 40% Morpheus precipitant mix 3

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.2	α = 90
b = 110.67	β = 90
c = 69.474	γ = 90

Symmetry
Space Group	C 2 2 21

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 PILATUS 6M		2022-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1	ELETTRA	11.2C

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	2.58	29.438	99.8	0.998	4.4	12.2		7832			49.5

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	2.58	2.7	99.2		0.942	4.4	12.3

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.581	29.438	7818	367	99.783	0.176	0.1726	0.18	0.236	0.24	random	51.123

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]
-0.242			1.351		-1.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.156
r_dihedral_angle_6_deg	15.708
r_dihedral_angle_2_deg	14.913
r_lrange_other	13.935
r_lrange_it	13.927
r_scangle_it	11.835
r_scangle_other	11.829
r_mcangle_other	9.785
r_mcangle_it	9.771
r_scbond_it	9.052
r_scbond_other	9.046
r_dihedral_angle_1_deg	8.422
r_mcbond_other	7.485
r_mcbond_it	7.484
r_angle_refined_deg	2.192
r_angle_other_deg	0.834
r_nbd_refined	0.22
r_nbtor_refined	0.189
r_symmetry_nbd_other	0.178
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.14
r_nbd_other	0.106
r_chiral_restr	0.1
r_symmetry_nbd_refined	0.093
r_symmetry_nbtor_other	0.086
r_gen_planes_refined	0.014
r_bond_refined_d	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1376
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MrBUMP	phasing