5KXD | pdb_00005kxd

Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 6.5

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291.15	0.1 M NaAc 0.1 M MES pH 6.5 30% (w/v) PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.096	α = 90
b = 104.271	β = 90
c = 148.739	γ = 90

Symmetry
Space Group	P 21 21 21

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 300 mm CCD	Vertical Focusing Mirror	2015-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.95	30	99.3	0.173	0.185	0.089	5.7	7.5		89308

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.01	98.6		0.508	0.782		7.6	7305

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 (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	5KXC	1.95	30	84025	4358	98.2	0.1798	0.1789	0.19	0.1981	0.21	RANDOM	22.833

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]
0.25			0.44		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.919
r_dihedral_angle_4_deg	22.669
r_dihedral_angle_3_deg	12.767
r_dihedral_angle_1_deg	6.927
r_mcangle_it	2.311
r_angle_refined_deg	1.566
r_mcbond_it	1.48
r_mcbond_other	1.466
r_angle_other_deg	0.998
r_chiral_restr	0.179

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.919
r_dihedral_angle_4_deg	22.669
r_dihedral_angle_3_deg	12.767
r_dihedral_angle_1_deg	6.927
r_mcangle_it	2.311
r_angle_refined_deg	1.566
r_mcbond_it	1.48
r_mcbond_other	1.466
r_angle_other_deg	0.998
r_chiral_restr	0.179
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7404
Nucleic Acid Atoms
Solvent Atoms	637
Heterogen Atoms	326

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.