9BH3 | pdb_00009bh3

Structure of apo Aggregatibacter actinomycetemcomitans SiaP protein

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	Drops consisting of 400 nL of mother-liquor and protein solution (AaSiaP at 20 mg/mL along with and without 0.75 mM Neu5Ac in SEC buffer) were mixed using the Mosquito Protein Crystallization System and the sitting-drop vapor-diffusion method and incubated at 20 C. Apo AaSiaP crystals that grew in SG1 conditions C11 (0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate, pH 6.5, 30% (w/v) PEG 8000)

Crystal Properties
Matthews coefficient	Solvent content
3.63	66.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.667	α = 90
b = 141.394	β = 112.491
c = 109.405	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	PIXEL	DECTRIS EIGER X 16M		2019-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.91840	Australian Synchrotron	MX2

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	2.58	48.64	100	0.995	6.3	3.6		61226

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	2.58	2.65			0.783	1.6

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	2.58	48.64	58058	3158	99.94	0.19069	0.18906	0.1945	0.21965	0.2184	RANDOM	61.518

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]
0.53		-0.9	1.09		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.228
r_long_range_B_refined	8.714
r_long_range_B_other	8.714
r_scangle_other	7.229
r_dihedral_angle_1_deg	6.093
r_mcangle_other	5.238
r_mcangle_it	5.233
r_scbond_it	4.686
r_scbond_other	4.656
r_mcbond_it	3.497
r_mcbond_other	3.484
r_angle_refined_deg	1.53
r_angle_other_deg	0.522
r_chiral_restr	0.072
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9608
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	8

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing