6RFZ | pdb_00006rfz

Photorhabdus laumondii lectin PLL2 in complex with D-glucose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	8% PEG 4000, 150 mM sodium acetate pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.498	α = 90
b = 71.099	β = 103.95
c = 86.221	γ = 90

Symmetry
Space Group	I 1 2 1

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 PILATUS3 2M		2018-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.8	47.39	99	0.288	0.903	3.4	3.8		35262			13.025

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	98.8		1.045	0.452	1.5	3.9

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	45.64	33419	1672	98.37	0.21156	0.21037	0.22	0.23497	0.24	RANDOM	15.456

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]
0.31		1.05	-0.81		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.45
r_dihedral_angle_3_deg	12.008
r_dihedral_angle_1_deg	7.746
r_dihedral_angle_4_deg	7.093
r_long_range_B_refined	3.403
r_long_range_B_other	3.052
r_angle_other_deg	2.388
r_angle_refined_deg	1.192
r_mcangle_it	0.652
r_mcangle_other	0.652
r_scangle_other	0.606
r_mcbond_it	0.385
r_mcbond_other	0.383
r_scbond_it	0.369
r_scbond_other	0.369
r_chiral_restr	0.042
r_bond_other_d	0.037
r_gen_planes_refined	0.004
r_gen_planes_other	0.004
r_bond_refined_d	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2616
Nucleic Acid Atoms
Solvent Atoms	361
Heterogen Atoms	77

Software

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