4EQH | pdb_00004eqh

Crystal structure of histidine triad nucleotide-binding protein 1 (HINT1) from human complexed with Trp-AMS

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6RHN	PDB ENTRY 6RHN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	25-28% PEG3350, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79	α = 90
b = 46.427	β = 95.24
c = 63.884	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	MARMOSAIC 300 mm CCD		2011-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.668	25	98.4	0.053	9.7	7.5		26559

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	1.668	1.73	96.7		0.489		7.3	2608

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 6RHN	1.668	24.348	1.35	25244	1270	93.4	0.145	0.1435	0.14	0.1729	0.16	16.6055

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]
1.234		0.1831	-1.1477		-0.0864

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.481
f_angle_d	1.25
f_chiral_restr	0.087
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1755
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	37

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
MOLREP	phasing

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.