3COQ | pdb_00003coq

Structural Basis for Dimerization in DNA Recognition by Gal4

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	298	40mM Mg(OAc)2, 25mM sodium phosphate, 5% PEG400, 5% MPD, pH 5.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.495	α = 90
b = 40.829	β = 95.88
c = 90.418	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298					M	MAD
2	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.2823,1.2830,1.2448	NSLS	X25
2	SYNCHROTRON	CHESS BEAMLINE F1		CHESS	F1

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
1,2	2.4	50	98.1	0.066	16.4	3.7		18311

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)
1,2	2.4	2.49	97		0.417		3.5	1758

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.4	28.94	14040	1304	96.91	0.213	0.207	0.2298	0.269	0.2839	RANDOM	48.172

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]
0.19		0.23	-0.17		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.995
r_dihedral_angle_3_deg	24.666
r_dihedral_angle_4_deg	19.743
r_dihedral_angle_1_deg	8.318
r_scangle_it	4.456
r_angle_refined_deg	3.337
r_scbond_it	3.053
r_mcangle_it	2.632
r_mcbond_it	1.604
r_nbtor_refined	0.341
r_nbd_refined	0.297
r_symmetry_vdw_refined	0.276
r_xyhbond_nbd_refined	0.195
r_symmetry_hbond_refined	0.177
r_chiral_restr	0.174
r_bond_refined_d	0.03
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1454
Nucleic Acid Atoms	814
Solvent Atoms	33
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
SOLVE	phasing
DENZO	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data collection
CNS	phasing