8R8A | pdb_00008r8a

Structure of the N-terminal domain of CMA in complex with N-acetyllactosamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	A0A1S4E5V9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	10% Peg Smear Medium, 0.1 M Mes pH 6.5, and 5 mM of CaCl2, MgCl2, CsCl2, CdCl2, NiCl2 and Zinc acetate transfered in 30% Peg Smear Medium 5mM CdCl2 for cryoprotection

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.696	α = 90
b = 36.782	β = 99.237
c = 94.786	γ = 90

Symmetry
Space Group	I 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 16M		2023-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 1

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	1.317	46.78	99.8	0.055	0.059	0.022	0.999	25.2	13.5		29695

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	1.32	1.34			0.369	0.4	0.153	0.969	5.7

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	1.317	46.778	29694	1503	99.798	0.146	0.1435	0.15	0.1858	0.19	13.471

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]
-0.245		-0.068	0.761		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.075
r_dihedral_angle_3_deg	14
r_lrange_it	11.386
r_lrange_other	10.265
r_scangle_it	8.283
r_scangle_other	8.277
r_scbond_it	6.411
r_scbond_other	6.406
r_dihedral_angle_1_deg	6.145
r_mcangle_it	5.852
r_mcangle_other	5.852
r_rigid_bond_restr	5.716
r_mcbond_it	4.445
r_mcbond_other	4.444
r_angle_refined_deg	1.721
r_dihedral_angle_2_deg	1.385
r_angle_other_deg	0.616
r_symmetry_metal_ion_refined	0.287
r_symmetry_nbd_refined	0.229
r_symmetry_nbd_other	0.214
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.193
r_nbd_other	0.188
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.142
r_metal_ion_refined	0.12
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	953
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	29

Software

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