4PZ4 | pdb_00004pz4

High-resolution crystal structure of the human CD44 hyaluronan binding domain in new space group

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	7	277	25% PEG 3350, 100 mM NACl, 100 mM HEPES, (5% DMSO), pH 7.0, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.271	α = 90
b = 70.271	β = 90
c = 286.458	γ = 120

Symmetry
Space Group	P 61 2 2

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	MARMOSAIC 300 mm CCD	K-B pair of biomorph mirrors for vertical and horizontal focusing	2011-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.000	APS	23-ID-D

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	1.598	286.458	99.3	0.063	26.4	12.8	56358	56356	1	1

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	1.598	1.604	80.4		0.49	0.516	5.3	12.1	455

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	1.6	60.86	56286	2864	99.18	0.1989	0.1974	0.195	0.2289	0.2262	RANDOM	18.407

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]
0.5	0.25		0.5		-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.396
r_dihedral_angle_4_deg	20.397
r_dihedral_angle_3_deg	13.383
r_dihedral_angle_1_deg	6.723
r_scangle_it	3.805
r_scbond_it	2.466
r_mcangle_it	1.593
r_angle_refined_deg	1.406
r_mcbond_it	0.869
r_chiral_restr	0.094

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.396
r_dihedral_angle_4_deg	20.397
r_dihedral_angle_3_deg	13.383
r_dihedral_angle_1_deg	6.723
r_scangle_it	3.805
r_scbond_it	2.466
r_mcangle_it	1.593
r_angle_refined_deg	1.406
r_mcbond_it	0.869
r_chiral_restr	0.094
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2373
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	84

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	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.