5BZL | pdb_00005bzl

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
2.17	43.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.095	α = 90
b = 81.95	β = 118.09
c = 32.277	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	PIXEL	DECTRIS PILATUS 6M		2013-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.23	81.95	96.4	0.037	20.3	3.3		39805

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.23	1.234	88.9		0.16		3.2	385

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.23	40.97	37426	2033	96.35	0.1736	0.1729	0.17	0.1877	0.19	RANDOM	12.349

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]
-0.1		-0.3	-0.01		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.902
r_dihedral_angle_4_deg	19.203
r_dihedral_angle_3_deg	10.906
r_dihedral_angle_1_deg	7.079
r_scangle_it	3.536
r_scbond_it	2.245
r_mcangle_it	1.515
r_angle_refined_deg	1.406
r_mcbond_it	0.825
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.902
r_dihedral_angle_4_deg	19.203
r_dihedral_angle_3_deg	10.906
r_dihedral_angle_1_deg	7.079
r_scangle_it	3.536
r_scbond_it	2.245
r_mcangle_it	1.515
r_angle_refined_deg	1.406
r_mcbond_it	0.825
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1171
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	26

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
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.