32OA | pdb_000032oa

The ultra-high-resolution hyaluronan-binding domain of mouse CD44

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	200 mM ammonium sulphate, 100 mM MES, 24% PEG5KMME

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.96	α = 90
b = 82.136	β = 117.884
c = 32.225	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 EIGER2 XE 16M		2020-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.7338	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	0.775	41.068	80.5	0.276	0.277	0.029	1	14.1	86.9		132017

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.775	0.826	9.3		5.997	6.072	0.932	0.672	1.6	39.4

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 (All)	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	0.775	41.068	132016	2015	80.463	0.111	0.1104	0.113	0.1156	0.1148	RANDOM	8.765

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]
0.001		0.006	-0.062		0.035

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.697
r_dihedral_angle_2_deg	12.894
r_dihedral_angle_3_deg	11.843
r_lrange_it	10.721
r_lrange_other	8.012
r_dihedral_angle_1_deg	7.596
r_rigid_bond_restr	5.857
r_scangle_it	5.379
r_scangle_other	5.377
r_scbond_other	4.027
r_scbond_it	3.802
r_mcangle_other	3.336
r_mcangle_it	3.327
r_mcbond_it	2.287
r_mcbond_other	2.285
r_angle_refined_deg	1.756
r_angle_other_deg	0.683
r_xyhbond_nbd_refined	0.311
r_nbd_refined	0.29
r_symmetry_xyhbond_nbd_refined	0.26
r_nbtor_refined	0.2
r_nbd_other	0.194
r_symmetry_nbd_other	0.193
r_symmetry_xyhbond_nbd_other	0.149
r_symmetry_nbd_refined	0.127
r_chiral_restr	0.113
r_symmetry_nbtor_other	0.096
r_bond_refined_d	0.012
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1171
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
STARANISO	data scaling
PHASER	phasing