6TSL | pdb_00006tsl

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

X-RAY DIFFRACTION

---

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 Na-acetate pH 5.0, 18% PEG 8000, 0.25 M sodium acetate, 10 mM CaCl2, 5 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.918	α = 90
b = 121.918	β = 90
c = 99.89	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		2014-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97908	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	46.7	99.7	0.097	0.103	0.033	0.999	10.7	9.7		86228

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	93.7		7.367	2.668	8.292	0.367	0.3	9.3

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	46.7	86189	4338	99.677	0.187	0.1866	0.19	0.203	0.21	26.914

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]
1.03	0.515		1.03		-3.342

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.92
r_dihedral_angle_4_deg	17.8
r_dihedral_angle_3_deg	13.81
r_dihedral_angle_1_deg	8.3
r_lrange_it	5.058
r_lrange_other	5.057
r_scangle_it	4.033
r_scangle_other	4.033
r_scbond_it	2.736
r_scbond_other	2.733
r_mcangle_other	2.554
r_mcangle_it	2.553
r_mcbond_it	1.9
r_mcbond_other	1.894
r_angle_refined_deg	0.837
r_angle_other_deg	0.607
r_symmetry_nbd_refined	0.293
r_symmetry_xyhbond_nbd_other	0.25
r_nbd_refined	0.207
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.171
r_nbd_other	0.159
r_xyhbond_nbd_refined	0.132
r_symmetry_metal_ion_refined	0.125
r_metal_ion_refined	0.122
r_symmetry_nbtor_other	0.108
r_symmetry_xyhbond_nbd_refined	0.103
r_gen_planes_refined	0.041
r_gen_planes_other	0.034
r_chiral_restr	0.014
r_bond_refined_d	0.013
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2310
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	74

Software

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