8SF5 | pdb_00008sf5

Promiscuous amino acid gamma synthase from Caldicellulosiruptor hydrothermalis in open conformation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	E4QC33

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	16% PEG 3350, 0.125 M Sodium Thiocyanate pH 8.0. Protein was 20 mg/mL in 50 mM HEPES pH 7.5. Four microliter drops were formed with a 1:1 mixture of protein and well solution. Crystals formed slowly over the course of 10 months

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.921	α = 90
b = 79.921	β = 90
c = 230.492	γ = 120

Symmetry
Space Group	P 31 2 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	CCD	RAYONIX MX-300		2022-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.3	45	99.9	0.126	0.999	13.6	10.7		38922

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	99.8		1.949	0.473	1.29	9.2

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	2.3	44.324	38898	2006	99.915	0.209	0.2073	0.21	0.243	0.24	58.219

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]
0.698	0.349		0.698		-2.264

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.508
r_dihedral_angle_4_deg	16.27
r_dihedral_angle_3_deg	14.486
r_dihedral_angle_1_deg	6.71
r_lrange_it	2.95
r_lrange_other	2.949
r_scangle_it	1.702
r_scangle_other	1.702
r_mcangle_it	1.561
r_mcangle_other	1.561
r_angle_refined_deg	1.305
r_angle_other_deg	1.165
r_scbond_it	1.032
r_scbond_other	1.032
r_mcbond_it	0.957
r_mcbond_other	0.957
r_nbd_refined	0.181
r_nbd_other	0.179
r_symmetry_nbd_refined	0.174
r_symmetry_nbd_other	0.172
r_symmetry_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.157
r_xyhbond_nbd_refined	0.144
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.05
r_bond_refined_d	0.004
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	6149
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms

Software

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