2DFY

Crystal structure of a cyclized protein fusion of LMO4 LIM domains 1 and 2 with the LIM interacting domain of LDB1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RUT	PDB ENTRY 1RUT WITH MULTIPLE CONFORMERS, SOLVENT AND ZINC ATOMS REMOVED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	296	1M AMMONIUM SULPHATE, 0.1M TRIS, 15% GLYCEROL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.333	α = 90
b = 61.333	β = 90
c = 93.019	γ = 120

Symmetry
Space Group	P 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	OSMIC MIRRORS	2005-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	1.65	50	99.4	0.034	36.3	3.9	46870	44295

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	1.65	1.69	99		0.33	2.2	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1RUT WITH MULTIPLE CONFORMERS, SOLVENT AND ZINC ATOMS REMOVED	1.65	10	46663	44295	2368	99.45	0.168	0.168	0.167	0.194	RANDOM	42.98

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.087
r_dihedral_angle_4_deg	16.105
r_dihedral_angle_3_deg	12.396
r_sphericity_free	9.039
r_dihedral_angle_1_deg	5.977
r_scangle_it	3.769
r_sphericity_bonded	3.594
r_scbond_it	2.831
r_rigid_bond_restr	2.204
r_mcangle_it	1.989
r_mcbond_it	1.755
r_angle_refined_deg	1.398
r_angle_other_deg	0.794
r_mcbond_other	0.627
r_symmetry_vdw_refined	0.207
r_nbd_refined	0.193
r_nbd_other	0.191
r_nbtor_refined	0.175
r_symmetry_vdw_other	0.159
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.092
r_nbtor_other	0.081
r_bond_refined_d	0.014
r_metal_ion_refined	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2420
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing