3O84 | pdb_00003o84

Structure of BasE N-terminal domain from Acinetobacter baumannii bound to 6-phenyl-1-(pyridin-4-ylmethyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O83	PDB ENTRY 3O83

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	287	5-15% PEG 8000, 5% MPD, 250-600 mM CaCl2, 50 mM BTP , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.534	α = 90
b = 143.312	β = 90
c = 148.815	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	113	CCD	ADSC QUANTUM 210		2009-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.9782	CHESS	A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.1	30	99.7	0.072	10.8	4	82723	82475		-3	32.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.2	97.9		0.425	1.8	3.34	10447

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3O83	2.1	29.8	78200	78200	4086	99.7	0.1865	0.1865	0.18521	0.18	0.2107	0.21	RANDOM	34.368

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]
1.41			0.67		-2.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.436
r_dihedral_angle_4_deg	17.139
r_dihedral_angle_3_deg	13.834
r_dihedral_angle_1_deg	5.705
r_scangle_it	3.002
r_scbond_it	1.735
r_mcangle_it	1.196
r_angle_refined_deg	1.182
r_mcbond_it	0.624
r_chiral_restr	0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.436
r_dihedral_angle_4_deg	17.139
r_dihedral_angle_3_deg	13.834
r_dihedral_angle_1_deg	5.705
r_scangle_it	3.002
r_scbond_it	1.735
r_mcangle_it	1.196
r_angle_refined_deg	1.182
r_mcbond_it	0.624
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6778
Nucleic Acid Atoms
Solvent Atoms	434
Heterogen Atoms	80

Software

Software
Software Name	Purpose
Adxv	data processing
MOLREP	phasing
REFMAC	refinement
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.