7C94

Crystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptide

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PHOTON FACTORY BEAMLINE BL-1A
Synchrotron site	Photon Factory
Beamline	BL-1A
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-03-04
Detector	DECTRIS EIGER X 4M
Wavelength(s)	1.1
Spacegroup name	P 1 21 1
Unit cell lengths	43.100, 42.960, 221.080
Unit cell angles	90.00, 91.37, 90.00

Refinement procedure

Resolution	44.200 - 2.840
R-factor	0.2231
Rwork	0.220
R-free	0.25530
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1a4j
RMSD bond length	0.003
RMSD bond angle	0.740
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASES
Refinement software	PHENIX (1.14_3260)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	44.200	44.200	3.020
High resolution limit [Å]	2.840	8.390	2.840
Rmerge	0.184	0.071	0.657
Rmeas	0.202	0.077	0.739
Number of reflections	19390	817	3129
<I/σ(I)>	7.74	17.57	2.04
Completeness [%]	98.8	97.8	96.1
Redundancy	5.852	5.737	4.708
CC(1/2)	0.988	0.997	0.748

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.1M Tris-HCl pH 7.5, 0.2M magnesium Acetate, 25% v/v PEG 3350