6OYY | pdb_00006oyy

Crystal structure of Mtb aspartate decarboxylase, pyrazinoic acid complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C45

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	290	MES, HEPES, PEG 3350, Ammonium Chloride

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.282	α = 90
b = 162.282	β = 90
c = 62.826	γ = 90

Symmetry
Space Group	P 41 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	130	PIXEL	DECTRIS PILATUS3 6M		2018-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D

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	2.7	21.92	99.7	0.999	16.48	15.7		23578

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	2.7	2.796	99.87		0.774	2.31

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	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	2C45	2.7	21.76	22440	1140	99.71	0.20159	0.19934	0.2	0.24666	0.25	RANDOM	56.54

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]
-0.71			-0.71		1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.979
r_dihedral_angle_4_deg	18.916
r_dihedral_angle_3_deg	14.601
r_long_range_B_refined	9.155
r_long_range_B_other	9.155
r_scangle_other	7.469
r_dihedral_angle_1_deg	6.953
r_mcangle_it	6.456
r_mcangle_other	6.455
r_scbond_it	5.006
r_scbond_other	5.006
r_mcbond_it	4.395
r_mcbond_other	4.393
r_angle_refined_deg	1.437
r_angle_other_deg	1.351
r_chiral_restr	0.068
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5262
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHENIX	phasing