4MRG

Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JCP	pdb entry 2JCP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	30% PEG MME 5000, 100 mM MES, 200 mM (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.85	α = 90
b = 81.58	β = 117.93
c = 32.13	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		2012-12-16	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)	R Sym I (Observed)	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	1.69	40.8	95.7	0.039	0.046	27.2	3.7	56490	56490			18.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.69	1.73	74.8		0.197	0.243	5.3	2.7	871

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2JCP	1.69	40.8	15170	778	96.66	0.1627	0.1604	0.206	RANDOM	10.718

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]
-0.39		-0.18	0.27		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.889
r_dihedral_angle_4_deg	19.259
r_dihedral_angle_3_deg	11.548
r_dihedral_angle_1_deg	7.046
r_scangle_it	4.015
r_scbond_it	2.544
r_angle_refined_deg	1.563
r_mcangle_it	1.434
r_mcbond_it	0.874
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.889
r_dihedral_angle_4_deg	19.259
r_dihedral_angle_3_deg	11.548
r_dihedral_angle_1_deg	7.046
r_scangle_it	4.015
r_scbond_it	2.544
r_angle_refined_deg	1.563
r_mcangle_it	1.434
r_mcbond_it	0.874
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1171
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	32

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

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.