4A75 | pdb_00004a75

The Lin28b Cold shock domain in complex with hexathymidine.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	0.75 mM protein-DNA complex (in 20 mM Tris/HCl, pH 7.5, 100 mM KCl, 2 mM MgCl2 and 1 mM DTT) and 0.1 mM Bis-Tris, pH 5.5, 15% (w/v) PEG 3350 and 0.1 M sodium thiocyanate as reservoir buffer

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.799	α = 90
b = 81.822	β = 90
c = 99.819	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY		BESSY	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.75	32.91	89.4	0.06	0.078	13.2	2.5		39188		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.75	1.85	87.8		0.39	3.3

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	OTHER	THROUGHOUT	NONE	1.75	32.91	40088	2110	100	0.17239	0.17105	0.21	0.19801	0.23	RANDOM	14.67

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]
-0.28			0.67		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.172
r_dihedral_angle_4_deg	17.295
r_dihedral_angle_3_deg	11.963
r_dihedral_angle_1_deg	6.292
r_scangle_it	4.778
r_scbond_it	3.59
r_mcangle_it	2.71
r_mcbond_it	1.731
r_angle_refined_deg	1.476
r_angle_other_deg	0.983
r_mcbond_other	0.476
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2734
Nucleic Acid Atoms	400
Solvent Atoms	506
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement