6FF3 | pdb_00006ff3

Crystal structure of Drosophila neural ectodermal development factor Imp-L1 with Human IGF-I

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CBP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	cp 10 mg/ml, 4-8% w/v PEG 6K, 5-20 mM MgCl2, 5 mM SB12, 0.1 M TRIS pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.03	α = 90
b = 94.15	β = 95.26
c = 48.36	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	PIXEL	DECTRIS PILATUS3 S 6M		2013-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.57	48.16	96.4	0.093	0.059	3.9	3.9		10666

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.57	2.64	97.6		0.783	0.47		4.1

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	4CBP	2.57	48.16	10666	535	95.65	0.23199	0.22938	0.23	0.2852	0.28	RANDOM	58.991

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]
3.14		0.3	-3.46		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.586
r_dihedral_angle_3_deg	24.866
r_dihedral_angle_4_deg	24.169
r_long_range_B_refined	11.001
r_long_range_B_other	11
r_scangle_other	7.04
r_dihedral_angle_1_deg	6.638
r_mcangle_it	6.208
r_mcangle_other	6.207
r_scbond_it	4.536
r_scbond_other	4.536
r_mcbond_it	4.107
r_mcbond_other	4.089
r_angle_refined_deg	1.676
r_angle_other_deg	0.835
r_chiral_restr	0.082
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1886
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing