4I75 | pdb_00004i75

Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase in complex with the NiTris metalorganic complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4I71	TbbIAGNH-363 complex

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.6	292	0.1M Tris, 23% PEGMME2000, 10mM Ni2SO4, pH 8.6, VAPOR DIFFUSION, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.7	α = 90
b = 134.89	β = 90
c = 60.99	γ = 90

Symmetry
Space Group	P 21 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	MARMOSAIC 225 mm CCD		2010-08-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

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	1.8	68	99.4	0.068	14.29	3.7	54442	54442		-3	25.787

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	94.7		0.561	0.66	2.6	3.5	3780

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 (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	TbbIAGNH-363 complex	1.8	48.8	54442	54442	2761	99.4	0.1825	0.1804	0.2	0.2232	0.24	RANDOM	20.222

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]
0.74			-0.96		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.025
r_dihedral_angle_4_deg	17.141
r_dihedral_angle_3_deg	15.04
r_sphericity_free	14.508
r_dihedral_angle_1_deg	6.243
r_scangle_it	3.979
r_scbond_it	2.577
r_angle_refined_deg	1.608
r_mcangle_it	1.437
r_angle_other_deg	1.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.025
r_dihedral_angle_4_deg	17.141
r_dihedral_angle_3_deg	15.04
r_sphericity_free	14.508
r_dihedral_angle_1_deg	6.243
r_scangle_it	3.979
r_scbond_it	2.577
r_angle_refined_deg	1.608
r_mcangle_it	1.437
r_angle_other_deg	1.164
r_mcbond_it	0.807
r_mcbond_other	0.272
r_chiral_restr	0.101
r_bond_refined_d	0.019
r_bond_other_d	0.004
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4972
Nucleic Acid Atoms
Solvent Atoms	492
Heterogen Atoms	51

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction

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.