9BJ7 | pdb_00009bj7

Crystal structure of the N-terminal truncated AbiV (residues 24-201)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		295	0.2 M Lithium sulfate, 0.1 M TRIS pH 8.5, 30% (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.444	α = 90.96
b = 106.901	β = 89.95
c = 146.228	γ = 95.02

Symmetry
Space Group	P 1

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 PILATUS3 S 6M		2020-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

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	2.64	146.21	92.9	0.089	0.106	0.055	0.998	8.1	3.5		122595

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	2.64	2.78		91.5	0.766	0.909	0.483	0.815		3.3

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 (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	2.64	106.7	116552	6013	92.89	0.2275	0.22537	0.2289	0.26836	0.2683	RANDOM	75.437

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]
-5.01	0.47	-0.38	7.28	0.14	-2.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.317
r_dihedral_angle_4_deg	24.7
r_dihedral_angle_3_deg	20.896
r_long_range_B_refined	11.591
r_long_range_B_other	11.591
r_scangle_other	9.127
r_dihedral_angle_1_deg	6.634
r_mcangle_it	6.473
r_mcangle_other	6.473
r_scbond_it	5.435
r_scbond_other	5.391
r_mcbond_it	4.037
r_mcbond_other	4.037
r_angle_refined_deg	1.741
r_angle_other_deg	1.342
r_chiral_restr	0.078
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	29942
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
XDS	data reduction
MOLREP	phasing