3TW2

High resolution structure of human histidine triad nucleotide-binding protein 1 (hHINT1)/AMP complex in a monoclinic space group

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KPF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	278	19% PEG 8000, 0.1M sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.421	α = 90
b = 46.449	β = 94.42
c = 64.034	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	CCD	MAR CCD 165 mm		2011-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8123	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.38	25.58	100	0.122	13.1	4.4	45932	45932		-3	11.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.38	1.45	84		0.291	3.4	2.8	5760

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1KPF	1.38	25.58	46364	43580	2320	99	0.12277	0.12277	0.12073	0.16148	RANDOM	17.709

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]
1.33		-0.02	-0.76		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.035
r_dihedral_angle_4_deg	14.196
r_dihedral_angle_3_deg	13.05
r_dihedral_angle_1_deg	5.793
r_scangle_it	4.208
r_scbond_it	3.027
r_mcangle_it	1.906
r_angle_refined_deg	1.479
r_rigid_bond_restr	1.44
r_mcbond_it	1.219

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.035
r_dihedral_angle_4_deg	14.196
r_dihedral_angle_3_deg	13.05
r_dihedral_angle_1_deg	5.793
r_scangle_it	4.208
r_scbond_it	3.027
r_mcangle_it	1.906
r_angle_refined_deg	1.479
r_rigid_bond_restr	1.44
r_mcbond_it	1.219
r_chiral_restr	0.104
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1767
Nucleic Acid Atoms
Solvent Atoms	409
Heterogen Atoms	23

Software

Software
Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.