4RDU

Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	289	0.08M sodium chloride, 45.00% 2-methyl-2,4-pentanediol, 0.012M spermine tetrahydrochloride, 0.1M sodium cacodylate pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.182	α = 84.13
b = 42.913	β = 77.33
c = 56.104	γ = 67.13

Symmetry
Space Group	P 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	MARMOSAIC 325 mm CCD	Vertical focusing mirror; double crystal Si(111) monochromator	2014-07-24	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.85	22.303	95.5	0.046	8	1.9	23348	23348			33.646

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)
1	1.85	1.9	94.1		0.271	0.271	2.5	1.9	1723

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1IG7	1.85	22.303	23315	1188	95.14	0.185	0.1829	0.2252	RANDOM	47.0789

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]
1.79	1.68	0.94	-3.44	-1.41	3.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.428
r_dihedral_angle_4_deg	23.005
r_dihedral_angle_3_deg	13.37
r_dihedral_angle_1_deg	4.955
r_angle_other_deg	1.409
r_angle_refined_deg	1.316
r_chiral_restr	0.1
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.428
r_dihedral_angle_4_deg	23.005
r_dihedral_angle_3_deg	13.37
r_dihedral_angle_1_deg	4.955
r_angle_other_deg	1.409
r_angle_refined_deg	1.316
r_chiral_restr	0.1
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1008
Nucleic Acid Atoms	1114
Solvent Atoms	233
Heterogen Atoms

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
PHASER	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.