3NAU | pdb_00003nau

Crystal structure of ZHX2 HD2 (zinc-fingers and homeoboxes protein 2, homeodomain 2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ECC	PDB ENTRY 2ecc

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	294	20% PEG 6000, 0.2M LiCl, HEPES pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.71	α = 90
b = 60.67	β = 95.34
c = 27.71	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	100	CCD	MARMOSAIC 225 mm CCD		2005-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.976	ESRF	BM14

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	2.7	30	100	0.111	15.4	5.6		4459		-1.5

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)
	2.7	2.8		100	0.451	3.1	5.6	449

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 (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 2ecc	2.7	28.38	4214	240	99.91	0.20664	0.20329	0.2	0.26684	0.26	RANDOM	35.638

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]
4.2		0.15	-3.53		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.475
r_dihedral_angle_3_deg	16.407
r_dihedral_angle_4_deg	14.874
r_scangle_it	6.397
r_dihedral_angle_1_deg	4.841
r_scbond_it	4.7
r_mcangle_it	3.647
r_mcbond_it	2.888
r_angle_refined_deg	0.902
r_angle_other_deg	0.784
r_mcbond_other	0.674
r_symmetry_vdw_other	0.249
r_nbd_refined	0.198
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.166
r_nbd_other	0.156
r_symmetry_vdw_refined	0.138
r_symmetry_hbond_refined	0.125
r_nbtor_other	0.084
r_chiral_restr	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	938
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	5

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling