3QGZ | pdb_00003qgz

Re-investigated high resolution crystal structure of histidine triad nucleotide-binding protein 1 (HINT1) from rabbit complexed with adenosine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	281	25% PEG 8000, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.747	α = 90
b = 39.747	β = 90
c = 141.83	γ = 90

Symmetry
Space Group	P 43 21 2

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		2009-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.038	MAX II	I911-2

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	1.1	39.74	99.2	0.087	18.7	17.5		47034		-3	8.7

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	1.1	1.16	97.5		0.676	4	13.5	6556

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	RIGID BODY REFINEMENT	THROUGHOUT	PDB entry 1RZY	1.1	38.27	44545	2371	98.97	0.14377	0.14377	0.1425	0.15	0.16772	0.17	RANDOM	17.569

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]
0.06			0.06		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.33
r_dihedral_angle_3_deg	13.941
r_dihedral_angle_4_deg	10.817
r_scangle_it	7.054
r_dihedral_angle_1_deg	6.24
r_scbond_it	5.363
r_mcangle_it	4.026
r_rigid_bond_restr	2.894
r_mcbond_it	2.755
r_angle_refined_deg	2.489

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.33
r_dihedral_angle_3_deg	13.941
r_dihedral_angle_4_deg	10.817
r_scangle_it	7.054
r_dihedral_angle_1_deg	6.24
r_scbond_it	5.363
r_mcangle_it	4.026
r_rigid_bond_restr	2.894
r_mcbond_it	2.755
r_angle_refined_deg	2.489
r_chiral_restr	0.153
r_bond_refined_d	0.027
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	873
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	19

Software

Software
Software Name	Purpose
MAR345	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	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.