3O1C | pdb_00003o1c

High resolution crystal structure of histidine triad nucleotide-binding protein 1 (Hint1) C38A mutant from rabbit complexed with Adenosine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	281	20% PEG 8000, 0.1M sodium acetate, 0.1M sodium cacodylate pH 6.5, protein concentration 10 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.965	α = 90
b = 39.965	β = 90
c = 141.7	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	RAYONIX MX-225	mirrors	2009-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	1.08	28.26	96.7	0.066	26.3	19.9		48586		-3	9.5

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)
	1.08	1.14	94.2		0.556	5	14.3	95611

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3LLJ	1.08	28.26	50494	46067	2481	96.15	0.13335	0.13335	0.13182	0.14	0.16285	0.17	RANDOM	20.525

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]
0.08			0.08		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.477
r_dihedral_angle_3_deg	13.316
r_dihedral_angle_4_deg	12.47
r_scangle_it	7.385
r_dihedral_angle_1_deg	6.541
r_scbond_it	5.621
r_mcangle_it	4.874
r_mcbond_it	3.314
r_angle_refined_deg	2.371
r_rigid_bond_restr	1.972

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.477
r_dihedral_angle_3_deg	13.316
r_dihedral_angle_4_deg	12.47
r_scangle_it	7.385
r_dihedral_angle_1_deg	6.541
r_scbond_it	5.621
r_mcangle_it	4.874
r_mcbond_it	3.314
r_angle_refined_deg	2.371
r_rigid_bond_restr	1.972
r_chiral_restr	0.147
r_bond_refined_d	0.028
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	883
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	21

Software

Software
Software Name	Purpose
MAR345	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.