2H8R | pdb_00002h8r

Hepatocyte Nuclear Factor 1b bound to DNA: MODY5 Gene Product

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IC8	PDB ENTRY 1IC8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	6%(v/v) PEG300, 5%(v/v) PEG8000, 8%(v/v) glycerol, 100mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.689	α = 90
b = 174.689	β = 90
c = 72.434	γ = 120

Symmetry
Space Group	H 3

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		2005-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	0.97923	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	3.2	27.9	93.9	0.088	0.083	28.8	6.3	12635	12582			57.24

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)
	3.2	3.31	63.4		0.313	0.273	3.35	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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 1IC8	3.2	20	2	12582	11992	637	93.26	0.22614	0.22292	0.19	0.2899	0.26	RANDOM	69.209

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]
5.43	2.72		5.43		-8.15

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	20.239
r_dihedral_angle_1_deg	12.042
r_scangle_it	8.674
r_scbond_it	5.745
r_angle_refined_deg	5.45
r_sphericity_bonded	5.174
r_mcangle_it	4.678
r_rigid_bond_restr	3.686
r_mcbond_it	2.542
r_symmetry_hbond_refined	0.47
r_nbd_refined	0.374
r_xyhbond_nbd_refined	0.294
r_chiral_restr	0.258
r_symmetry_vdw_refined	0.236
r_bond_refined_d	0.079
r_gen_planes_refined	0.02
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2916
Nucleic Acid Atoms	814
Solvent Atoms	7
Heterogen Atoms

Software

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