9VLR | pdb_00009vlr

Acinetobacter baumannii membrane-bound lytic transglycosylase B

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ANR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	25% (w/v) PEG-1500, 0.1M MMT Buffer pH6.5

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.49	α = 90
b = 75.49	β = 90
c = 175.36	γ = 90

Symmetry
Space Group	P 43 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	80	PIXEL	DECTRIS EIGER X 9M		2021-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.979	PAL/PLS	5C (4A)

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	1.79	29.33	99.94	0.999	20.21	26.6		48656

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	1.79	1.854			0.72

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	1.79	29.329	48651	2433	99.938	0.183	0.1824	0.1884	0.2046	0.2099	27.713

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]
0.325			0.325		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.762
r_dihedral_angle_3_deg	13.957
r_dihedral_angle_1_deg	5.408
r_lrange_it	4.951
r_lrange_other	4.861
r_scangle_it	4.186
r_scangle_other	4.185
r_scbond_it	3.121
r_scbond_other	3.117
r_mcangle_other	2.916
r_mcangle_it	2.915
r_mcbond_it	2.278
r_mcbond_other	2.278
r_dihedral_angle_2_deg	1.592
r_angle_refined_deg	1.487
r_angle_other_deg	0.719
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.22
r_nbd_other	0.209
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.192
r_symmetry_xyhbond_nbd_other	0.118
r_symmetry_xyhbond_nbd_refined	0.104
r_symmetry_nbtor_other	0.075
r_symmetry_nbd_refined	0.068
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2405
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling