5UVD | pdb_00005uvd

Crystal structure of an antigenic nucleotidyltransferase-like protein from Paracoccidioides brasiliensis

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	0.25 M MgCl2, 25% PEG 4000, 0.1 M Tris-HCl pH 7.0 - 8,0
2	VAPOR DIFFUSION, HANGING DROP		293.15	0.25 M MgCl2, 25% PEG 4000, 0.1 M Tris-HCl pH 7.0 - 8,0 Crystal was incubated in a cryo-soaking solution containing 100 mM NaI and 10% (v/v) ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.5
2.1	41.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.649	α = 90
b = 51.105	β = 90
c = 121.19	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M	collimating mirror and toroidal bendable mirror	2013-05-24	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MAR CCD 165 mm	collimating mirror and toroidal bendable mirror	2014-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.4587	LNLS	W01B-MX2
2	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.4587	LNLS	W01B-MX2

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
2	1.68	31.77	86.1	0.039	18.5	1.9		39751		-3	22.5

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)
2	1.68	1.71	68.9		0.172	3.7	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	1.86	47.09	16999	895	97.85	0.16216	0.15909	0.17	0.22168	0.23	RANDOM	17.673

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]
-0.93			2.25		-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.061
r_dihedral_angle_4_deg	20.954
r_dihedral_angle_3_deg	13.741
r_long_range_B_refined	5.573
r_dihedral_angle_1_deg	5.236
r_long_range_B_other	5.236
r_scangle_other	3.578
r_scbond_it	2.308
r_scbond_other	2.308
r_mcangle_other	1.909
r_mcangle_it	1.908
r_angle_refined_deg	1.878
r_mcbond_it	1.338
r_mcbond_other	1.325
r_angle_other_deg	1.075
r_chiral_restr	0.111
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1718
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data processing
DENZO	data processing
XDS	data scaling
HKL-2000	data scaling
AutoSol	phasing