8Q7U | pdb_00008q7u

Photorhabdus laumondii lectin PLL in complex with alpha-methyl-fucoside

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5C9L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7.5	277	20 mM Tris/HCl 150 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.217	α = 90
b = 89.184	β = 90
c = 158.773	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 EIGER X 16M		2022-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9763	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	45.555	100	0.084	0.024	0.999	18.6	13.5		66905

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69	100		1.003	0.288	0.828	2.8	12.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	45.555	66903	3371	99.981	0.163	0.1625	0.1764	0.1796	0.1919	18.573

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]
1.048			-0.381		-0.667

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.746
r_dihedral_angle_3_deg	11.52
r_dihedral_angle_2_deg	8.302
r_dihedral_angle_1_deg	8.068
r_lrange_it	5.151
r_lrange_other	4.995
r_scangle_it	4.015
r_scangle_other	4.014
r_mcangle_other	2.774
r_mcangle_it	2.77
r_scbond_it	2.747
r_scbond_other	2.746
r_mcbond_it	2.021
r_mcbond_other	2.021
r_angle_refined_deg	1.679
r_angle_other_deg	0.618
r_symmetry_nbd_other	0.191
r_nbd_refined	0.184
r_nbtor_refined	0.177
r_nbd_other	0.159
r_symmetry_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.157
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2726
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms	31

Software

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