2JCR | pdb_00002jcr

The hyaluronan binding domain of murine CD44 in a Type B complex with an HA 8-mer

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		CO-CRYSTALS OF THE CD44/HA8 COMPLEX WERE PREPARED AFTER ADDITION OF HA8 (2MM FINAL CONCENTRATION) TO THE 0.5 MM PROTEIN SOLUTION FOLLOWED BY MIXING 1:1 WITH WELL SOLUTIONS CONTAINING 25% (W/V) PEG 3350 AND 100MM NACL IN 100MM HEPES BUFFERED AT PH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.12	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.8	α = 90
b = 82.1	β = 118
c = 32.4	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	BRUKER	MIRRORS	2005-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR

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	2	28.6	92.3	0.11	10.4	2.5		9641

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	2	2.05	67.5		0.24	3.6	1.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2JCQ	2	28.61	8114	407	88.5	0.179	0.175	0.18	0.254	0.26	RANDOM	9.88

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]
-0.97		-0.88	0.78		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.989
r_dihedral_angle_4_deg	16.704
r_dihedral_angle_3_deg	14.059
r_dihedral_angle_1_deg	6.667
r_sphericity_free	3.04
r_scangle_it	2.161
r_scbond_it	1.382
r_angle_refined_deg	1.28
r_sphericity_bonded	0.923
r_angle_other_deg	0.855
r_mcangle_it	0.755
r_rigid_bond_restr	0.711
r_mcbond_it	0.559
r_symmetry_vdw_other	0.255
r_nbd_refined	0.196
r_nbd_other	0.195
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.184
r_nbtor_refined	0.172
r_mcbond_other	0.164
r_xyhbond_nbd_refined	0.161
r_nbtor_other	0.081
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1172
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	99

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM	data reduction
SAINT	data reduction
SADABS	data scaling
XSCALE	data scaling
MOLREP	phasing