9I4G | pdb_00009i4g

Blood Type B-converting alpha-1,3-galactosidase PpaGal from Pedobacter panaciterrae in complex with D-galactose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	SwissModel

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.4	293	0.2 M lithium citrate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.011	α = 90
b = 129.025	β = 90.129
c = 108.404	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 EIGER X 16M		2024-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97626	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.978	107.011	99.4	0.21	0.234	0.103	0.989	6.4	5		60001		-3	31.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.978	3.03	99.2		0.68	0.772	0.358	0.834	2.1	4.5

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	2.98	107.011	59905	2967	99.439	0.228	0.2266	0.2166	0.2608	0.2599	36.266

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]
1.429		0.739	-2.209		0.776

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.658
r_dihedral_angle_6_deg	12.745
r_dihedral_angle_1_deg	7.427
r_dihedral_angle_2_deg	7.402
r_lrange_it	2.197
r_lrange_other	2.197
r_angle_refined_deg	1.3
r_mcangle_it	1.142
r_mcangle_other	1.142
r_scangle_it	1.067
r_scangle_other	1.067
r_mcbond_it	0.625
r_mcbond_other	0.625
r_scbond_it	0.575
r_scbond_other	0.575
r_angle_other_deg	0.458
r_nbd_other	0.223
r_symmetry_nbd_refined	0.21
r_symmetry_nbd_other	0.206
r_nbd_refined	0.186
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.13
r_symmetry_xyhbond_nbd_refined	0.099
r_symmetry_nbtor_other	0.083
r_ncsr_local_group_2	0.063
r_chiral_restr	0.06
r_ncsr_local_group_3	0.06
r_ncsr_local_group_1	0.056
r_ncsr_local_group_6	0.056
r_ncsr_local_group_4	0.055
r_ncsr_local_group_5	0.053
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18556
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
PHASER	phasing
XDS	data scaling
XDS	data reduction
MxCuBE	data collection