3CA7 | pdb_00003ca7

High Resolution Crystal Structure of the EGF domain of Spitz

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JL9	PDB ENTRY 1JL9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	294	15mM ammonium sulphate, 0.1M MES pH 6.5, 24% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.305	α = 90
b = 36.154	β = 103.09
c = 25.362	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 300 mm CCD	3.0 UNDULATOR	2007-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D

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	1.499	50	91.6	0.047	16.3	5.3		7284		-3	20.6

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)
	1.499	1.55	56.6		0.21	4.6	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 1JL9	1.5	30.5	7634	7284	350	91.5	0.201	0.2	0.2	0.236	0.23	RANDOM	20.66

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]
-0.45		-0.92	0.96		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.263
r_dihedral_angle_3_deg	13.785
r_dihedral_angle_4_deg	11.741
r_dihedral_angle_1_deg	6.683
r_scangle_it	3.222
r_scbond_it	2.152
r_mcangle_it	1.535
r_angle_refined_deg	1.165
r_mcbond_it	1.083
r_nbtor_refined	0.313
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.169
r_symmetry_vdw_refined	0.162
r_xyhbond_nbd_refined	0.115
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	406
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms

Software

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