2E46 | pdb_00002e46

Crystal Structure Analysis of the clock protein EA4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E9P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	293	9% ethlene glycol, 1M ammonium fluoride, 100mM Bis-Tris, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.5	α = 90
b = 59.5	β = 90
c = 112.072	γ = 90

Symmetry
Space Group	P 41 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	CCD	MAR CCD 165 mm		2003-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	1	SPring-8	BL44B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	20	99.9		6.9		9519

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	1E9P	2.3	19.76	8710	493	100	0.21229	0.20795	0.2237	0.28522	0.2888	RANDOM	44.995

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]
0.74			0.74		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.907
r_dihedral_angle_3_deg	20.546
r_dihedral_angle_4_deg	18.345
r_dihedral_angle_1_deg	9.6
r_scangle_it	6.318
r_scbond_it	4.535
r_angle_refined_deg	2.902
r_mcangle_it	2.655
r_mcbond_it	1.684
r_xyhbond_nbd_refined	0.451
r_chiral_restr	0.356
r_nbtor_refined	0.33
r_symmetry_vdw_refined	0.324
r_symmetry_hbond_refined	0.322
r_nbd_refined	0.277
r_symmetry_metal_ion_refined	0.05
r_bond_refined_d	0.036
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1181
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	3

Software

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