12VT | pdb_000012vt

Y318A Human Aconitate Decarboxylase 1 mutant, apo

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	12UX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.8	295	100 mM Tris pH 8.8, 35% PEG 4000, 200 mM CaOAc, 200 nL drops, 2:1 protein:reservoir

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.889	α = 90
b = 110.165	β = 90
c = 76.11	γ = 90

Symmetry
Space Group	P 21 21 2

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 9M		2025-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.92021	NSLS-II	17-ID-1

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	1.62	34.55	94.4	0.136	0.28	0.072	0.995	8.4	13.9		80794			19.2

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	1.62	1.82	46.3		2.35	2.52	0.664	0.55	1.5	14.2

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.62	34.55	80793	4198	74.036	0.163	0.1604	0.1603	0.2019	0.2019	RANDOM	19.536

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]
-0.316			0.262		0.054

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.817
r_dihedral_angle_3_deg	13.664
r_dihedral_angle_2_deg	8.92
r_dihedral_angle_1_deg	6.402
r_lrange_it	4.829
r_lrange_other	4.666
r_scangle_it	2.349
r_scangle_other	2.348
r_mcangle_it	1.634
r_mcangle_other	1.634
r_angle_refined_deg	1.538
r_scbond_it	1.436
r_scbond_other	1.435
r_mcbond_it	0.974
r_mcbond_other	0.973
r_angle_other_deg	0.538
r_symmetry_metal_ion_refined	0.254
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.217
r_xyhbond_nbd_refined	0.19
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.173
r_metal_ion_refined	0.166
r_nbd_other	0.161
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.075
r_symmetry_xyhbond_nbd_other	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	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	7084
Nucleic Acid Atoms
Solvent Atoms	837
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing