3T8J

Structural analysis of thermostable S. solfataricus pyrimidine-specific nucleoside hydrolase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	298	100 mM Bicine, 1.5 M Ammonium sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 194.94	α = 90
b = 194.94	β = 90
c = 42.86	γ = 120

Symmetry
Space Group	P 64 2 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	ADSC QUANTUM 315r		2009-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.976	ESRF	ID23-1

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	1.6	100	99.9	0.07	35.64		63536	63536	-3	-3	23.745

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	1.6	1.7	100		0.319	11.91

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	PDB ENTRY 3T8I	1.6	100	63536	63536	3224	99.94	0.1565	0.1565	0.1558	0.1704	RANDOM	30.1405

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]
-0.62	-0.31		-0.62		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.67
r_dihedral_angle_4_deg	14.755
r_dihedral_angle_3_deg	12.585
r_dihedral_angle_1_deg	6.217
r_scangle_it	3.356
r_scbond_it	2.09
r_angle_refined_deg	1.399
r_mcangle_it	1.278
r_angle_other_deg	0.933
r_mcbond_it	0.704

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.67
r_dihedral_angle_4_deg	14.755
r_dihedral_angle_3_deg	12.585
r_dihedral_angle_1_deg	6.217
r_scangle_it	3.356
r_scbond_it	2.09
r_angle_refined_deg	1.399
r_mcangle_it	1.278
r_angle_other_deg	0.933
r_mcbond_it	0.704
r_mcbond_other	0.215
r_chiral_restr	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2484
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	1

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 R01GM133198.