8QSW | pdb_00008qsw

Crystal structure of SPOUT1/CENP-32 | A356N catalytic site mutant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.09 M NaF, NaBr, NaI; 0.1 M Sodium HEPES, MOPS (acid) pH 7.5 and 30 % Ethylene glycol, PEG 8K

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.24	α = 90
b = 80.694	β = 90
c = 136.363	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 9M		2014-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92000	Diamond	I04-1

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	2.5	37.62	97.33	0.06425	0.07257	0.03278	0.999	11.22	4.5		14321

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	2.5	2.69			0.4695	0.5331	0.2461	0.963	2.72

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	2.5	37.62	13609	711	97.29	0.20546	0.20275	0.2089	0.2623	0.271	RANDOM	84.116

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]
1.83			5.58		-7.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.198
r_long_range_B_refined	10.353
r_long_range_B_other	10.351
r_dihedral_angle_2_deg	9.49
r_dihedral_angle_1_deg	8.163
r_scangle_other	8.094
r_mcangle_it	7.104
r_mcangle_other	7.101
r_scbond_it	5.513
r_scbond_other	5.51
r_mcbond_it	4.819
r_mcbond_other	4.816
r_angle_refined_deg	1.701
r_angle_other_deg	0.575
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
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	2204
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms

Software

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