3D3J | pdb_00003d3j

Crystal structure of human Edc3p

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3D3K	PDB ENTRY 3D3K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	PEG 6000, sodium cacodylate, magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.741	α = 90
b = 119.741	β = 90
c = 93.923	γ = 90

Symmetry
Space Group	I 4 2 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	ADSC QUANTUM 315		2006-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.8					9673	9673

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 3D3K	2.8	20	8273	419	99.97	0.23197	0.22901	0.2277	0.29062	0.2812	RANDOM	76.149

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]
3.94			3.94		-7.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.375
r_dihedral_angle_3_deg	16.586
r_dihedral_angle_4_deg	8.721
r_dihedral_angle_1_deg	4.954
r_angle_refined_deg	0.978
r_scangle_it	0.792
r_scbond_it	0.472
r_mcangle_it	0.396
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.233
r_mcbond_it	0.21
r_nbd_refined	0.181
r_xyhbond_nbd_refined	0.171
r_symmetry_hbond_refined	0.159
r_chiral_restr	0.066
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1791
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing