8JBD | pdb_00008jbd

Crystal structure of Adenylosuccinate lyase from Thermus thermophilus HB8, TtPurB

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	293	0.1M Sodium acetate trihydrate (pH 4.6), 1.0M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.657	α = 90
b = 158.657	β = 90
c = 151.634	γ = 120

Symmetry
Space Group	P 65 2 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	CCD	MARMOSAIC 225 mm CCD		2007-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.0	SPring-8	BL26B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.37	50	100	0.077	30.8	11.2		86898

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.37	2.45	100		0.353	6.83	11.3

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.38	19.992	45475	2262	99.743	0.207	0.2047	0.21	0.2485	0.25	43.549

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]
0.001	0.001		0.001		-0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.648
r_dihedral_angle_4_deg	19.528
r_dihedral_angle_3_deg	18.217
r_lrange_other	10.621
r_lrange_it	10.609
r_scangle_it	8.306
r_scangle_other	8.302
r_dihedral_angle_1_deg	8.068
r_mcangle_it	5.928
r_mcangle_other	5.927
r_scbond_it	5.579
r_scbond_other	5.574
r_mcbond_it	4.366
r_mcbond_other	4.366
r_angle_refined_deg	1.714
r_angle_other_deg	1.405
r_symmetry_nbd_refined	0.33
r_symmetry_xyhbond_nbd_refined	0.241
r_nbd_refined	0.233
r_nbd_other	0.216
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.023
r_bond_refined_d	0.011
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	4860
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing