6TSM | pdb_00006tsm

Marasmius oreades agglutinin (MOA) in complex with the truncated PVVRAHS synthetic substrate

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, 20% PEG 8000, 0.2 M sodium acetate, 10 mM CaCl2, 5 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
3.3	63.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.155	α = 90
b = 122.155	β = 90
c = 100.02	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		2015-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97239	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	1.4	46.8	99.8	0.145	0.152	0.035	0.999	11.6	19.2		87357

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	1.4	1.42	97.2		5.335	5.489	1.266	0.362	0.362	17.8

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	1.4	46.8	87323	4388	99.8	0.18	0.179	0.19	0.1978	0.21	20.883

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]
0.547	0.274		0.547		-1.775

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.253
r_dihedral_angle_3_deg	14.169
r_dihedral_angle_4_deg	14.028
r_dihedral_angle_1_deg	8.229
r_lrange_it	4.381
r_lrange_other	4.38
r_scangle_it	3.377
r_scangle_other	3.377
r_scbond_it	2.237
r_scbond_other	2.229
r_mcangle_it	2.177
r_mcangle_other	2.177
r_mcbond_it	1.497
r_mcbond_other	1.482
r_angle_refined_deg	0.876
r_angle_other_deg	0.605
r_symmetry_nbd_refined	0.315
r_symmetry_xyhbond_nbd_other	0.252
r_nbd_refined	0.218
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.174
r_nbd_other	0.174
r_metal_ion_refined	0.156
r_symmetry_metal_ion_refined	0.146
r_xyhbond_nbd_refined	0.138
r_symmetry_xyhbond_nbd_refined	0.112
r_symmetry_nbtor_other	0.101
r_gen_planes_refined	0.042
r_gen_planes_other	0.035
r_chiral_restr	0.016
r_bond_refined_d	0.013
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2305
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	74

Software

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