6Z6C | pdb_00006z6c

Crystal structurel of FleA lectin in complex with a monovalent inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4AH4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	50 mM L-Arginin, 50 mm L-Glutamate, 28% PEG Smear Broad and 5% glycerol (BCS screen 1-32)

Crystal Properties
Matthews coefficient	Solvent content
2.19	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.117	α = 103.083
b = 46.893	β = 98.536
c = 80.173	γ = 108.512

Symmetry
Space Group	P 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 EIGER X 16M		2018-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97857	SOLEIL	PROXIMA 1

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	42.54	99.2	0.052	0.061	0.032	0.998	16.1	6.5		115240

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	96.4		0.3	0.388	0.236	0.0963	3.1	4.7

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	4AH4	1.4	42.534	115179	5702	99.132	0.12	0.1185	0.13	0.1579	0.16	18.21

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]
0.957	-0.134	0.455	-0.471	-0.199	-0.277

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.277
r_dihedral_angle_4_deg	12.22
r_dihedral_angle_3_deg	11.691
r_dihedral_angle_1_deg	7.476
r_rigid_bond_restr	3.999
r_lrange_it	3.555
r_lrange_other	3.377
r_scangle_it	3.358
r_scangle_other	3.357
r_scbond_it	2.891
r_scbond_other	2.891
r_mcangle_other	2.399
r_mcangle_it	2.398
r_mcbond_it	2.104
r_mcbond_other	2.098
r_angle_refined_deg	1.82
r_angle_other_deg	1.565
r_nbd_other	0.237
r_nbd_refined	0.199
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.164
r_xyhbond_nbd_refined	0.136
r_metal_ion_refined	0.123
r_symmetry_xyhbond_nbd_refined	0.119
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.086
r_ncsr_local_group_1	0.077
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4909
Nucleic Acid Atoms
Solvent Atoms	713
Heterogen Atoms	184

Software

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