5BZG

Crystal structure of the murine CD44 hyaluronan binding domain complex with a small molecule

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	PEG MME 5000, MES, (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.987	α = 90
b = 81.744	β = 118.205
c = 32.236	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	NOIR-1		2013-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.000	ALS	4.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.16	9.64	94.8	0.116	0.135	11.8	3.787		7318		-3	19.588

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.16	2.21	57		0.401	0.481	2.76

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.19	9.64	6800	378	98.32	0.1935	0.191	0.2416	RANDOM	12.274

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]
-1.23		-0.82	0.98		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.068
r_dihedral_angle_4_deg	16.828
r_dihedral_angle_3_deg	12.105
r_dihedral_angle_1_deg	6.642
r_scangle_it	2.815
r_scbond_it	1.7
r_angle_refined_deg	1.321
r_mcangle_it	0.998
r_mcbond_it	0.534
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.068
r_dihedral_angle_4_deg	16.828
r_dihedral_angle_3_deg	12.105
r_dihedral_angle_1_deg	6.642
r_scangle_it	2.815
r_scbond_it	1.7
r_angle_refined_deg	1.321
r_mcangle_it	0.998
r_mcbond_it	0.534
r_chiral_restr	0.093
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1171
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	21

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.