8R8C | pdb_00008r8c

Structure of the N-terminal domain of CMA from Cucumis melo in complex with N-acetylgalactosamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8R8A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	12% Peg Smear Medium 0.1M Mes pH 6.5 5 mM of CaCl2, MgCl2, CsCl2, CdCl2, NiCl2 and Zinc acetate and GalNAc

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.613	α = 90
b = 36.86	β = 99.166
c = 94.813	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 9M		2023-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.98011	SOLEIL	PROXIMA 2

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	1.55	35.68	99.7	0.052	0.064	0.037	0.998	14.4	5.2		18279			19

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	1.55	1.58			0.496	0.618	0.364	0.857	2.9

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	1.55	35.68	18278	905	99.667	0.165	0.1629	0.18	0.204	0.21	17.55

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]
-0.871		0.034	1.355		-0.471

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.837
r_dihedral_angle_3_deg	10.821
r_dihedral_angle_1_deg	7.209
r_lrange_it	5.658
r_lrange_other	5.615
r_scangle_it	4.608
r_scangle_other	4.605
r_dihedral_angle_2_deg	4.259
r_scbond_it	3.151
r_scbond_other	3.148
r_mcangle_it	3.025
r_mcangle_other	3.023
r_mcbond_it	2.109
r_mcbond_other	2.104
r_angle_refined_deg	1.893
r_angle_other_deg	0.669
r_symmetry_nbd_refined	0.278
r_symmetry_xyhbond_nbd_refined	0.216
r_nbd_refined	0.207
r_symmetry_nbd_other	0.205
r_nbd_other	0.18
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.144
r_metal_ion_refined	0.131
r_xyhbond_nbd_other	0.123
r_symmetry_metal_ion_refined	0.103
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.091
r_bond_refined_d	0.013
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	963
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	33

Software

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