1XOD

Crystal structure of X. tropicalis Spred1 EVH-1 domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EVH	pdb entries 1EVH, 1I7A, 1QC6
experimental model	PDB	1I7A	pdb entries 1EVH, 1I7A, 1QC6
experimental model	PDB	1QC6	pdb entries 1EVH, 1I7A, 1QC6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	PEG 3350, potassium fluoride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.811	α = 90
b = 38.193	β = 95.68
c = 79.907	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 4	mirrors	2004-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2	0.975	SRS	PX14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.15	79	97.7	0.069	19.4	3.9	68977	68977			7.84

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.17	94.5		0.351	3.99	3.5	3330

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entries 1EVH, 1I7A, 1QC6	1.15	79.06	68977	68977	3471	97.69	0.155	0.15538	0.154	0.177	random	9.283

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]
0.13		-0.17	0.06		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.147
r_scangle_it	2.68
r_sphericity_free	2.217
r_sphericity_bonded	1.855
r_scbond_it	1.752
r_mcangle_it	1.536
r_angle_refined_deg	1.335
r_rigid_bond_restr	0.947
r_mcbond_it	0.94
r_angle_other_deg	0.833
r_symmetry_vdw_refined	0.487
r_symmetry_vdw_other	0.324
r_nbd_other	0.26
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.196
r_xyhbond_nbd_refined	0.171
r_nbtor_other	0.085
r_chiral_restr	0.079
r_gen_planes_other	0.019
r_gen_planes_refined	0.012
r_bond_refined_d	0.009
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1694
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms	6

Software

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