6YQD

Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.41 A in P212121 space group

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	281	8 % w/v PEG8000, 0.1 M Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.921	α = 90
b = 74.113	β = 90
c = 77.249	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS 6M-F		2018-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	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	1.407	77.25	98.8	0.073	0.079	0.03	0.999	18.2	12.5		42522			11.6

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	1.407	1.43	75.7		0.715	0.846	0.439	0.755	2.1

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	3TW2	1.407	53.48	42457	2092	98.673	0.102	0.1003	0.1428	17.947

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]
-0.771			0.182		0.589

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.084
r_dihedral_angle_4_deg	16.681
r_dihedral_angle_3_deg	12.144
r_dihedral_angle_1_deg	6.291
r_scangle_it	5.603
r_scangle_other	5.602
r_rigid_bond_restr	5.325
r_lrange_it	5.219
r_scbond_it	5.21
r_scbond_other	5.21
r_lrange_other	4.384
r_mcangle_it	2.463
r_mcangle_other	2.463
r_angle_refined_deg	2.008
r_mcbond_other	1.989
r_mcbond_it	1.988
r_angle_other_deg	1.665
r_nbd_refined	0.266
r_symmetry_nbd_other	0.201
r_symmetry_nbd_refined	0.191
r_nbd_other	0.189
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.164
r_chiral_restr	0.142
r_symmetry_xyhbond_nbd_refined	0.109
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1685
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing