7F7Q

Enterococcus faecalis GH31 alpha-N-acetylgalactosaminidase D455A in complex with p-nitrophenyl alpha-N-acetylgalactosaminide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	25% PEG3350, 0.2 M ammonium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.875	α = 90
b = 83.394	β = 90
c = 146.329	γ = 90

Symmetry
Space Group	P 21 21 21

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 2M		2020-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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	1.42	50	98	0.067	0.069	0.019	1	24.5	13.3		184729

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.5	94.7		1.044	0.29	0.766	2.7	13.5

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	6M76	1.42	42.139	184632	9317	97.837	0.175	0.1743	0.1963	22.221

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]
-0.588			-0.524		1.112

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.84
r_dihedral_angle_4_deg	16.405
r_dihedral_angle_3_deg	12.396
r_dihedral_angle_1_deg	7.222
r_lrange_it	5.159
r_lrange_other	5.031
r_angle_refined_deg	1.726
r_angle_other_deg	1.548
r_scangle_it	1.387
r_scangle_other	1.387
r_mcangle_it	0.945
r_mcangle_other	0.944
r_scbond_it	0.921
r_scbond_other	0.921
r_mcbond_other	0.543
r_mcbond_it	0.542
r_nbd_refined	0.211
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.186
r_nbd_other	0.185
r_symmetry_nbd_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_other	0.125
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7020
Nucleic Acid Atoms
Solvent Atoms	792
Heterogen Atoms	72

Software

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