6YQM | pdb_00006yqm

Human histidine triad nucleotide-binding protein 1 (hHINT1) complexed with dGMP and refined to 1.02 A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TW2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	281	16 % (w/v) PEG 4000, 0.1 M sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.658	α = 90
b = 46.434	β = 94.244
c = 64.102	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS3 2M		2020-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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	1.02	39.963	99.1	0.042	0.056	0.037	0.999	14.1	3.8		116020			5.1

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	1.02	1.04	93.6		0.466	0.63	0.422	0.785	2.1	3.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3TW2	1.02	39.96	116016	6128	99.056	0.113	0.1118	0.11	0.1356	0.14	11.705

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]
-0.117		-0.011	-0.047		0.163

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.209
r_dihedral_angle_4_deg	14.186
r_dihedral_angle_3_deg	12.428
r_rigid_bond_restr	8.289
r_lrange_it	7.017
r_lrange_other	7.016
r_dihedral_angle_1_deg	6.398
r_mcbond_other	5.931
r_mcbond_it	5.926
r_mcangle_it	5.524
r_mcangle_other	5.524
r_scangle_it	4.804
r_scangle_other	4.802
r_scbond_it	4.508
r_scbond_other	4.506
r_angle_refined_deg	2.403
r_angle_other_deg	1.991
r_nbd_other	0.369
r_nbd_refined	0.323
r_xyhbond_nbd_refined	0.273
r_symmetry_nbd_refined	0.27
r_symmetry_xyhbond_nbd_refined	0.213
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.173
r_chiral_restr	0.143
r_symmetry_nbtor_other	0.102
r_bond_refined_d	0.026
r_bond_other_d	0.021
r_gen_planes_refined	0.012
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1773
Nucleic Acid Atoms
Solvent Atoms	483
Heterogen Atoms	30

Software

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