8QSV | pdb_00008qsv

Crystal structure of SPOUT1/CENP-32 bound to SAM

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		using an experimentally determined model currently being processed for deposition (D_1292133583)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.06 M MgCl2, CaCl2 or 0.09 M NaF, NaBr, NaI with 0.1 M Imidazole, MES (acid) pH 6.5 and 30 % Ethylene glycol, PEG 8K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.07	α = 90
b = 80.83	β = 90
c = 135.69	γ = 90

Symmetry
Space Group	C 2 2 21

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 EIGER2 XE 16M		2014-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97000	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.62	55.01	99.08	0.08553	0.0932	0.0365	0.998	16.11	6.5		12626

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.62	2.88	98.02		0.6634	0.7196	0.2761	0.947	3.81	6.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.62	55.01	12000	628	99.09	0.20662	0.2028	0.2083	0.2802	0.2763	RANDOM	83.661

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]
4.02			3.72		-7.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.501
r_dihedral_angle_2_deg	10.633
r_long_range_B_refined	9.332
r_long_range_B_other	9.33
r_dihedral_angle_1_deg	7.886
r_scangle_other	7.166
r_mcangle_it	6.573
r_mcangle_other	6.571
r_scbond_it	4.783
r_scbond_other	4.781
r_mcbond_other	4.376
r_mcbond_it	4.375
r_angle_refined_deg	1.583
r_angle_other_deg	0.524
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	2151
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
xia2	data scaling
PHENIX	phasing