7PZG

Phocaeicola vulgatus sialic acid esterase at 1.44 Angstrom resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	18 % (w/v) PEG 3350, 200 mM sodium malonate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.269	α = 90
b = 90.15	β = 99.289
c = 76.579	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 XE 16M		2021-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	1.44	70.434	97.7	1	18.3	6.8		168248

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	1.44	1.46			0.712

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6njc	1.44	70.434	168177	8262	97.573	0.178	0.177	0.203	22.426

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]
-0.072		0.685	-0.424		0.258

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.925
r_dihedral_angle_4_deg	13.982
r_dihedral_angle_3_deg	12.062
r_lrange_it	7.143
r_lrange_other	7.141
r_dihedral_angle_1_deg	6.392
r_scangle_it	4.37
r_scangle_other	4.37
r_scbond_it	2.956
r_scbond_other	2.955
r_mcangle_it	2.526
r_mcangle_other	2.525
r_mcbond_it	1.853
r_mcbond_other	1.848
r_angle_refined_deg	1.835
r_angle_other_deg	1.529
r_symmetry_nbd_refined	0.276
r_nbd_refined	0.229
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.175
r_symmetry_nbd_other	0.17
r_nbd_other	0.164
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.1
r_symmetry_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6350
Nucleic Acid Atoms
Solvent Atoms	696
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing