Experiment: 3N9R

Class II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with N-(4-hydroxybutyl)-phosphoglycolohydroxamic acid, a competitive inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C52

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	8.5	298	12% PEG 1000, 12% PEG 8000, 0.2 M Calcium Acetate,50 mM Tris/HOAc, pH 8.5, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.4	α = 98.5
b = 104.4	β = 90
c = 111.9	γ = 90

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 315		2009-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0809	NSLS	X29A

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	1.798	46.631	96	0.087	7	3	205157	205157

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.9	94.4		0.3	0.3	2.3	3	29609

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	3C52	1.8	41.529	1.19	398819	31924	93.48	0.162	0.158	0.1584	0.203	0.2011	28.685

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]
-2.123	-0.151	-0.299	3.533	-1.178	-1.41

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.333
f_angle_d	0.983
f_chiral_restr	0.061
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18336
Nucleic Acid Atoms
Solvent Atoms	2783
Heterogen Atoms	144

Software

Software
Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling