6TSO | pdb_00006tso

Marasmius oreades agglutinin (MOA) inhibited by cadmium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EF2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293.15	0.1 M cacodylate/HCl pH 6.5, 16% PEG 8000, 0.2 M sodium acetate, 1 mM CdCl2, 10 mM CaCl2, 12.5% DMSO, 5 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.752	α = 90
b = 120.752	β = 90
c = 99.541	γ = 120

Symmetry
Space Group	P 63 2 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 PILATUS 6M		2013-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	2.0664	ESRF	ID29

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	2.1	46.3	92.6	0.196	0.218	0.094	0.995	7.6	5.1		44615

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	2.1	2.15	84.8		1.65	1.85	0.818	0.518

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	3EF2	2.1	46.3	23997	1204	92.503	0.195	0.193	0.2	0.2291	0.23	32.886

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]
1.365	0.683		1.365		-4.428

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.243
r_dihedral_angle_3_deg	13.573
r_dihedral_angle_4_deg	13.248
r_dihedral_angle_1_deg	8.225
r_lrange_it	5.561
r_lrange_other	5.554
r_scangle_it	4.378
r_scangle_other	4.377
r_mcangle_it	3.275
r_mcangle_other	3.274
r_scbond_it	3.003
r_scbond_other	3.002
r_mcbond_it	2.548
r_mcbond_other	2.546
r_angle_refined_deg	1.576
r_angle_other_deg	1.322
r_symmetry_nbd_refined	0.308
r_symmetry_xyhbond_nbd_refined	0.24
r_nbd_refined	0.206
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.133
r_nbd_other	0.131
r_symmetry_metal_ion_refined	0.098
r_metal_ion_refined	0.091
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_chiral_restr	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2278
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	108

Software

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