6TSN | pdb_00006tsn

Marasmius oreades agglutinin (MOA), papain back.swap W208Q-Q276W variant

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, 14% PEG 8000, 0.2 M calcium acetate, 10% DMSO, 5 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
3.3	63.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.615	α = 90
b = 121.615	β = 90
c = 100.032	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	CCD	MARMOSAIC 225 mm CCD		2012-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8726	ESRF	ID23-2

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	1.6	46.6	94.8	0.127	0.145	0.051	0.998	14.1	3.9		104686

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	1.6	1.63	77.6		1.749	2.359	1.572	0.265		2.9

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	1.6	46.6	55866	2756	96.55	0.186	0.1852	0.2	0.2091	0.22	18.138

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]
0.679	0.339		0.679		-2.203

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.495
r_dihedral_angle_4_deg	14.071
r_dihedral_angle_3_deg	13.032
r_dihedral_angle_1_deg	8.915
r_lrange_it	4.125
r_lrange_other	4.023
r_scangle_it	3.108
r_scangle_other	3.107
r_scbond_it	2.086
r_scbond_other	2.086
r_mcangle_it	1.928
r_mcangle_other	1.928
r_mcbond_it	1.415
r_mcbond_other	1.413
r_angle_refined_deg	0.96
r_angle_other_deg	0.877
r_symmetry_nbd_refined	0.381
r_nbd_refined	0.215
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.171
r_metal_ion_refined	0.161
r_nbd_other	0.157
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.127
r_symmetry_metal_ion_refined	0.127
r_symmetry_nbtor_other	0.111
r_gen_planes_refined	0.04
r_gen_planes_other	0.034
r_bond_refined_d	0.013
r_chiral_restr	0.012
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2280
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	110

Software

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