9BJ5 | pdb_00009bj5

Crystal structure of the HEPN family member AbiV (P212121 space group)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		295	0.1 M Tris-HCl pH 8.0, 1.8 M potassium sodium tartrate, 0.6 M sodium bromide

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.693	α = 90
b = 79.168	β = 90
c = 136.137	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH		2018-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	0.91908	CLSI	08B1-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.55	50	99.9	0.104	35	13.8		26667

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	2.55	2.64	98.7		0.877	0.934	2.3	9.9

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.55	42.31	25290	1307	99.66	0.22129	0.21891	0.2218	0.26749	0.2671	RANDOM	67.534

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]
-6.72			2.19		4.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.95
r_dihedral_angle_3_deg	21.002
r_dihedral_angle_4_deg	18.113
r_long_range_B_other	8.936
r_long_range_B_refined	8.935
r_dihedral_angle_1_deg	6.817
r_scangle_other	6.65
r_mcangle_it	5.865
r_mcangle_other	5.865
r_scbond_it	4.121
r_scbond_other	4.121
r_mcbond_it	3.705
r_mcbond_other	3.705
r_angle_refined_deg	1.846
r_angle_other_deg	1.364
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
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	4782
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
XDS	data reduction
AutoSol	phasing