8A47 | pdb_00008a47

IdeS 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	1Y08

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294.15	0.12 M monosaccharides mix (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D- Xylose; 0.2M N-Acetyl-D-Glucosamine), 0.1 M buffer system 3 (Tris (base); BICINE; pH 8.5), 30 % v/v precipitant mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)

Crystal Properties
Matthews coefficient	Solvent content
4.08	69.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 217.558	α = 90
b = 108.448	β = 90.059
c = 63.093	γ = 90

Symmetry
Space Group	C 1 2 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 4M	Vertical CRL	2021-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.338	48.53	97.7	0.229	0.255	0.112	5.3	4.96		60351

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	2.34	2.38	98.8		0.877	0.978	0.426	0.335	1	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1Y08	2.338	48.529	60350	3049	97.398	0.173	0.1712	0.16	0.2031	0.19	36.18

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]
0.77		-1.549	8.708		-9.478

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.924
r_dihedral_angle_3_deg	15.053
r_dihedral_angle_1_deg	7.671
r_lrange_it	7.108
r_lrange_other	7.108
r_dihedral_angle_2_deg	6.497
r_scangle_it	5.195
r_scangle_other	5.195
r_mcangle_it	4.876
r_mcangle_other	4.875
r_scbond_it	3.568
r_scbond_other	3.568
r_mcbond_it	3.434
r_mcbond_other	3.431
r_angle_refined_deg	1.448
r_angle_other_deg	0.499
r_symmetry_nbd_refined	0.313
r_nbd_refined	0.197
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.178
r_nbd_other	0.176
r_ncsr_local_group_1	0.131
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.078
r_chiral_restr	0.07
r_chiral_restr_other	0.016
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5791
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	185

Software

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