7PZH

Phocaeicola vulgatus sialic acid esterase at 2.06 Angstrom resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6NJC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulphate, 0.1 M MOPS/HEPES-Na pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.233	α = 90
b = 93.233	β = 90
c = 353.623	γ = 120

Symmetry
Space Group	P 61

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 X 16M		2021-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97624	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	2.06	80.74	100	0.998	11.2	20.5		106903

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	2.06	2.1			0.54

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	2.06	80.742	106769	5355	99.988	0.187	0.185	0.2258	37.958

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]
-0.037			-0.037		0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.977
r_dihedral_angle_4_deg	16.72
r_dihedral_angle_3_deg	16.037
r_dihedral_angle_1_deg	7.614
r_lrange_it	6.546
r_lrange_other	6.546
r_scangle_it	5.054
r_scangle_other	5.051
r_mcangle_it	4.566
r_mcangle_other	4.566
r_scbond_it	3.606
r_scbond_other	3.602
r_mcbond_it	3.517
r_mcbond_other	3.517
r_angle_refined_deg	1.646
r_angle_other_deg	1.32
r_nbd_refined	0.218
r_nbd_other	0.209
r_symmetry_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.196
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_other	0.099
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12619
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms	62

Software

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