3VD6

Both Zn Fingers of GATA1 Bound to Palindromic DNA Recognition Site, P21 Crystal Form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DFX	PDB ENTRY 3DFX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.2M ammonium acetate, 0.1M BISTRIS, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.331	α = 90
b = 37.401	β = 98.51
c = 65.484	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	MAR scanner 345 mm plate		2011-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	1.98	15	99.5	0.049	19.1	3.5	18281	18281			53.2

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	1.98	2.01	99.9		0.58		3.4	893

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3DFX	1.98	14.9	18203	18203	887	98.83	0.2196	0.2182	0.2468	RANDOM	55.616

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]
-2.91		-3.22	0.27		1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.671
r_dihedral_angle_3_deg	10.097
r_dihedral_angle_4_deg	9.388
r_dihedral_angle_1_deg	3.986
r_scangle_it	2.844
r_scbond_it	2.029
r_mcangle_it	1.655
r_angle_refined_deg	1.08
r_angle_other_deg	0.935
r_mcbond_it	0.917

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.671
r_dihedral_angle_3_deg	10.097
r_dihedral_angle_4_deg	9.388
r_dihedral_angle_1_deg	3.986
r_scangle_it	2.844
r_scbond_it	2.029
r_mcangle_it	1.655
r_angle_refined_deg	1.08
r_angle_other_deg	0.935
r_mcbond_it	0.917
r_mcbond_other	0.179
r_chiral_restr	0.044
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	756
Nucleic Acid Atoms	814
Solvent Atoms	93
Heterogen Atoms	7

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.