4PZ3 | pdb_00004pz3

High-resolution crystal structure of the human CD44 hyaluronan binding domain complex with undefined peptides

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	6.5	277	30% PEG MME 5000, 100 mM MES, 200 mM (NH4)2SO4, 5%DMSO, pH 6.5, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.498	α = 90
b = 60.288	β = 113.4
c = 75.134	γ = 90

Symmetry
Space Group	C 1 2 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	PSI PILATUS 6M	mirrors	2012-11-17	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	1.083	44.676	97.1	0.031	21.2	3.1	123233	122395

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	1.083	1.086	69.3		0.154	0.284	5.4	1.9	834

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	1.083	44.67	122393	6171	97.12	0.1668	0.1662	0.1659	0.1774	0.1775	RANDOM	11.604

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]
0.09		0.04	-0.24		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.438
r_dihedral_angle_4_deg	13.742
r_dihedral_angle_3_deg	11.252
r_dihedral_angle_1_deg	7.141
r_scangle_it	3.133
r_scbond_it	2.013
r_mcangle_it	1.519
r_angle_refined_deg	1.511
r_mcbond_it	0.887
r_chiral_restr	0.212

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.438
r_dihedral_angle_4_deg	13.742
r_dihedral_angle_3_deg	11.252
r_dihedral_angle_1_deg	7.141
r_scangle_it	3.133
r_scbond_it	2.013
r_mcangle_it	1.519
r_angle_refined_deg	1.511
r_mcbond_it	0.887
r_chiral_restr	0.212
r_bond_refined_d	0.012
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2364
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	27

Software

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

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.