8UX7 | pdb_00008ux7

Dioclea megacarpa lectin (DmegA) complexed with X-Man

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GDF	Dioclea violacea lectin

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	0.8M Potassium sodium tartrate tetrahydrate, 0.1M Tris pH 8.5, 0.5% PEGME 5000

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.35	α = 90
b = 109.414	β = 90
c = 126.364	γ = 90

Symmetry
Space Group	I 2 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 2M		2022-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.46	LNLS	W01B-MX2

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	2.2	46.661	100	0.088	0.092	0.025	1	21.6	13.1		31790

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	2.2	2.27		100	1.148	1.193	0.322	0.853		13.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.2	46.661	31752	1593	99.852	0.203	0.2006	0.21	0.2483	0.25	50.893

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]
-0.02			0.007		0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.591
r_dihedral_angle_6_deg	16.566
r_dihedral_angle_3_deg	13.958
r_lrange_it	9.756
r_lrange_other	9.745
r_dihedral_angle_1_deg	8.496
r_scangle_it	7.22
r_scangle_other	7.219
r_mcangle_other	6.135
r_mcangle_it	6.134
r_scbond_it	4.956
r_scbond_other	4.955
r_mcbond_it	4.372
r_mcbond_other	4.368
r_angle_refined_deg	1.477
r_angle_other_deg	0.498
r_nbd_refined	0.222
r_symmetry_nbd_other	0.205
r_symmetry_nbd_refined	0.2
r_nbtor_refined	0.182
r_metal_ion_refined	0.161
r_xyhbond_nbd_refined	0.149
r_nbd_other	0.148
r_symmetry_xyhbond_nbd_refined	0.122
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	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	3548
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
Coot	model building