Experiment: 2QL2

Crystal Structure of the basic-helix-loop-helix domains of the heterodimer E47/NeuroD1 bound to DNA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MDY	pdb entry 1MDY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.6	291	0.1 mM Imidazole, 0.2 M ammonium citrate dibasic, and 22 % PEG 4000, pH 7.6, EVAPORATION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.31	α = 90
b = 169.54	β = 90
c = 52.24	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	MAR scanner 345 mm plate	sagittal focusing crystal and vertical focusing double mirror	2006-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.000	APS	22-BM

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	2.5	169.546	97.7	0.076	0.076	5.7	7.2		18832		1	76

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)
	2.5	2.64	94.8		0.77	0.77	1	7.1	2594

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-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 1MDY	2.5	55.8	19270	18781	1884	97.5	0.248	0.2443	0.289	0.2819	random	56.998

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]
-8.549			-10.084		18.633

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_d	1.154
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1751
Nucleic Acid Atoms	1300
Solvent Atoms	41
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data processing
CNS	refinement
PDB_EXTRACT	data extraction
AUTOMAR	data collection
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing