12VQ | pdb_000012vq

H103A Human Aconitate Decarboxylase 1 mutant, apo

X-RAY DIFFRACTION

---

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 drop, 2:1 protein:reservoir

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.824	α = 90
b = 110.018	β = 90
c = 75.844	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	1.42	34.5	95.4	0.176	0.189	0.049	0.998	10.1	13.9		129811			16.1

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	1.42	1.54	51.9		2.43	2.62	0.696	0.598	1.4	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	1.42	34.5	129811	6630	80.408	0.152	0.1503	0.1503	0.1813	0.1813	RANDOM	16.789

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]
-0.067			0.092		-0.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.594
r_dihedral_angle_3_deg	13.84
r_dihedral_angle_2_deg	10.316
r_dihedral_angle_1_deg	6.3
r_lrange_it	5.358
r_lrange_other	5.142
r_scangle_it	2.659
r_scangle_other	2.659
r_mcangle_it	1.735
r_mcangle_other	1.734
r_angle_refined_deg	1.73
r_scbond_it	1.674
r_scbond_other	1.672
r_mcbond_it	1.067
r_mcbond_other	1.065
r_angle_other_deg	0.603
r_symmetry_nbd_refined	0.264
r_nbd_other	0.238
r_nbd_refined	0.234
r_xyhbond_nbd_refined	0.205
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.179
r_metal_ion_refined	0.162
r_symmetry_xyhbond_nbd_other	0.124
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.077
r_symmetry_metal_ion_refined	0.043
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7088
Nucleic Acid Atoms
Solvent Atoms	1040
Heterogen Atoms	26

Software

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