8Q5U | pdb_00008q5u

Endoglycosidase S2 in complex with IgG1 Fc

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6E58
experimental model	PDB	3AVE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	Morpheus (Molecular Dimensions) conditon G12: 0.1 M carboxylic acids(0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate tetrahydrate; 0.2M Sodium oxamate); 0.1 M buffer system 3(Tris (base); BICINE); pH 8.5; 37.5 v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 228.775	α = 90
b = 228.775	β = 90
c = 161.629	γ = 90

Symmetry
Space Group	P 43 21 2

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		2023-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	3	49.91	100	0.187	0.191	0.036	1	12.6	27.5		85926			77

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.05	100		2.614	2.668	0.527	0.64	0.5

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	3	49.91	85849	4376	99.956	0.218	0.2161	0.22	0.2516	0.25	100.098

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]
-0.691			-0.691		1.382

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.787
r_dihedral_angle_6_deg	13.837
r_dihedral_angle_2_deg	6.77
r_dihedral_angle_1_deg	6.462
r_lrange_it	6.25
r_lrange_other	6.244
r_scangle_it	2.648
r_scangle_other	2.648
r_mcangle_it	2.428
r_mcangle_other	2.428
r_scbond_it	1.496
r_scbond_other	1.496
r_mcbond_it	1.41
r_mcbond_other	1.41
r_angle_refined_deg	0.957
r_angle_other_deg	0.526
r_xyhbond_nbd_refined	0.203
r_symmetry_nbd_other	0.195
r_nbd_refined	0.182
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.169
r_symmetry_nbd_refined	0.167
r_nbd_other	0.16
r_metal_ion_refined	0.11
r_ncsr_local_group_1	0.108
r_ncsr_local_group_2	0.104
r_ncsr_local_group_5	0.104
r_ncsr_local_group_6	0.1
r_ncsr_local_group_3	0.095
r_ncsr_local_group_4	0.09
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.059
r_symmetry_xyhbond_nbd_other	0.024
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20629
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	258

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
MOLREP	phasing