7WU8

Crystal structure of Harmonin-homology domain 2 (HHD2) of human RTEL1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	277	20mM Tris pH7.4, 250mM NaCl, 5% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.64	α = 90
b = 60.96	β = 95.64
c = 79.71	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	PIXEL	DECTRIS PILATUS 6M-F	Toroidal mirror	2020-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9763	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.599	48.336	96.8	0.053	0.999	13.48	3.47		80150		-3	31.52

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.599	1.6	95.3		0.64	0.802	1.73

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-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	AF-Q9NZ71-F1	1.599	48.156	80146	2100	96.76	0.177	0.1765	0.2012	27.133

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]
0.174		1.443	0.144		-0.592

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.695
r_dihedral_angle_4_deg	19.823
r_dihedral_angle_3_deg	13.978
r_lrange_it	7.214
r_lrange_other	6.992
r_scangle_it	5.872
r_scangle_other	5.871
r_dihedral_angle_1_deg	4.576
r_scbond_it	3.848
r_scbond_other	3.847
r_mcangle_other	3.758
r_mcangle_it	3.756
r_mcbond_it	2.657
r_mcbond_other	2.649
r_angle_other_deg	2.34
r_angle_refined_deg	1.895
r_nbd_refined	0.246
r_symmetry_nbd_other	0.206
r_nbd_other	0.201
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.158
r_chiral_restr	0.108
r_symmetry_xyhbond_nbd_other	0.102
r_xyhbond_nbd_other	0.076
r_symmetry_nbtor_other	0.069
r_bond_other_d	0.036
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4388
Nucleic Acid Atoms
Solvent Atoms	735
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing