8BDU

H33 variant of DoBi scaffold based on PIH1D1 N-terminal domain

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	1 M (NH4)2SO4 1% (w/v) PEG3350 0.1 M Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
	76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.131	α = 90
b = 123.131	β = 90
c = 190.106	γ = 90

Symmetry
Space Group	I 41 2 2

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 PILATUS 6M		2019-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976260	PETRA III, EMBL c/o DESY	P13 (MX1)

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	2.47	47.53	69	0.126	0.136	0.036	0.999	14.8	12.6		18374

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	2.47	2.71	14.8		3.429	3.846	1.216	0.224	0.8	12.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	7AVC	2.471	47.53	18374	910	69.158	0.222	0.223	0.219	0.255	Random selection	81.639

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]
0.299			0.299		-0.599

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.435
r_lrange_other	19.356
r_lrange_it	19.353
r_dihedral_angle_6_deg	16.606
r_mcangle_other	14.056
r_mcangle_it	14.037
r_scangle_it	13.481
r_scangle_other	13.477
r_dihedral_angle_2_deg	10.028
r_mcbond_it	9.921
r_mcbond_other	9.896
r_scbond_it	9.466
r_scbond_other	9.462
r_dihedral_angle_1_deg	6.366
r_angle_refined_deg	1.755
r_angle_other_deg	0.572
r_symmetry_xyhbond_nbd_refined	0.228
r_nbd_refined	0.218
r_symmetry_nbd_other	0.206
r_symmetry_nbd_refined	0.201
r_nbtor_refined	0.189
r_nbd_other	0.187
r_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.093
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2071
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing