7PTB

Crystal structure of the SPD-2 domain of human CEP192

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		292.15	100 nl protein solution and 100 nl of reservoir solution which was 0.1 M Na-Acetate pH 5.3, 3.9 M ammonium ni-trate. Crystals were mounted in 0.1 M Na-Acetate pH 4.6, 1 M ammonium nitrate, 30% glycerol.

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.588	α = 90
b = 104.588	β = 90
c = 90.214	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS3 6M		2018-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.97835	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.08	90.6	100	0.024	19.7	18.6		33669

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.08	2.14	100		0.357		2.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.08	90.58	32002	1629	99.99	0.21252	0.21197	0.22364	RANDOM	45.671

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]
0.32	0.16		0.32		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.097
r_dihedral_angle_4_deg	13.437
r_dihedral_angle_3_deg	12.009
r_dihedral_angle_1_deg	6.702
r_long_range_B_refined	4.552
r_long_range_B_other	4.367
r_mcangle_it	2.343
r_mcangle_other	2.343
r_scangle_other	1.673
r_mcbond_other	1.264
r_mcbond_it	1.263
r_angle_refined_deg	1.171
r_angle_other_deg	1.029
r_scbond_it	0.9
r_scbond_other	0.898
r_chiral_restr	0.036
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
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	2516
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
CRANK2	phasing