3GNN | pdb_00003gnn

Crystal structure of nicotinate-nucleotide pyrophosphorylase from Burkholderi pseudomallei

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	HAMPTON CRYSTAL SCREEN CONDITION E8, 1.5 M NACL, 10% ETHANOL WITH 25% GLYCEROL AS CRYO-PROTECTANT, 28.7 MG/ML PROTEIN, CRYSTAL ID 109334E8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.978	α = 90
b = 57.414	β = 106.74
c = 66.243	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100				2008-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97934	APS	23-ID-D

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	2.25	50	98.9	0.068	21.998	3.8		27262

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)
	2.25	2.33	97.7		0.589	2.27	3.7	2650

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.25	39.14	27260	1366	98.67	0.217	0.214	0.21	0.273	0.27	RANDOM	48.358

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]
1.08		2.07	-2.44		2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.522
r_dihedral_angle_4_deg	19.676
r_dihedral_angle_3_deg	19.167
r_dihedral_angle_1_deg	6.585
r_scangle_it	4.725
r_scbond_it	2.895
r_mcangle_it	2.016
r_angle_refined_deg	1.791
r_mcbond_it	1.101
r_angle_other_deg	1.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.522
r_dihedral_angle_4_deg	19.676
r_dihedral_angle_3_deg	19.167
r_dihedral_angle_1_deg	6.585
r_scangle_it	4.725
r_scbond_it	2.895
r_mcangle_it	2.016
r_angle_refined_deg	1.791
r_mcbond_it	1.101
r_angle_other_deg	1.074
r_mcbond_other	0.232
r_chiral_restr	0.109
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3776
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	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.