1Z56 | pdb_00001z56

Co-Crystal Structure of Lif1p-Lig4p

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	Tris-HCl, Sodium Chloride, Dithiothreitol, PEG 6000, 2-(N-morpholino)ethanesulfonic acid, Ethylene Glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
5	75.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 247.617	α = 90
b = 247.617	β = 90
c = 98.416	γ = 120

Symmetry
Space Group	P 64 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	MARRESEARCH	SI-111 DOUBLE MONOCHROMATOR	2004-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13		ESRF	ID13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	3.92	49.2	99.8	0.175	0.175	5.7	10.1	16493	16475		2.5

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)
	3.92	3.99	99.6		0.799	0.799

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SIRAS	THROUGHOUT	3.92	49.2	15638	15638	832	99.8	0.403	0.4	0.4	0.467	0.46	RANDOM	107.705

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]
1.31	0.65		1.31		-1.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.914
r_dihedral_angle_3_deg	25.971
r_dihedral_angle_4_deg	20.912
r_dihedral_angle_1_deg	10.166
r_scangle_it	2.151
r_angle_refined_deg	2.13
r_angle_other_deg	1.987
r_scbond_it	1.203
r_mcangle_it	1.042
r_mcbond_it	0.596
r_nbd_refined	0.33
r_symmetry_vdw_refined	0.325
r_nbtor_refined	0.324
r_nbd_other	0.323
r_xyhbond_nbd_refined	0.257
r_nbtor_other	0.254
r_symmetry_hbond_refined	0.218
r_chiral_restr	0.132
r_mcbond_other	0.094
r_bond_refined_d	0.016
r_bond_other_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4164
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
SHARP	phasing