6YH0 | pdb_00006yh0

Marasmius oreades agglutinin (MOA) in complex with the truncated PVPRAHS 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 pH 6.5, 0.2 M Sodium acetate, 22% PEG 8000, 10 mM CaCl2, 5 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.244	α = 90
b = 121.244	β = 90
c = 99.913	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	0.972385	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	1.56	105	100	0.048	0.166	0.037	0.999	12.3	19.6		61848			23.9

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	1.56	1.59	100		1	1	1	0.362		15

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	1.56	51.882	61844	3149	99.981	0.175	0.174	0.19	0.1993	0.21	26.788

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]
0.826	0.413		0.826		-2.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.351
r_dihedral_angle_4_deg	21.864
r_dihedral_angle_3_deg	15.391
r_dihedral_angle_1_deg	7.522
r_lrange_it	5.318
r_lrange_other	5.317
r_scangle_it	4.579
r_scangle_other	4.55
r_scbond_it	3.11
r_scbond_other	3.109
r_mcangle_other	2.947
r_mcangle_it	2.945
r_mcbond_it	2.254
r_mcbond_other	2.179
r_angle_refined_deg	1.824
r_angle_other_deg	1.484
r_symmetry_nbd_refined	0.299
r_nbd_refined	0.217
r_metal_ion_refined	0.178
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.176
r_nbd_other	0.155
r_xyhbond_nbd_refined	0.137
r_symmetry_metal_ion_refined	0.103
r_symmetry_xyhbond_nbd_refined	0.101
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.06
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	2308
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	94

Software

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