Experiment: 3TC1

Crystal Structure of Octaprenyl Pyrophosphate Synthase from Helicobacter pylori

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	277	15% PEG 3350, 100mM sodium acetate, 200mM MgCl2, pH 4.8, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.33	α = 90
b = 109.33	β = 90
c = 103.41	γ = 90

Symmetry
Space Group	P 41 21 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	IMAGE PLATE	RIGAKU RAXIS		2008-12-18	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS		2009-05-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.97901	Photon Factory	BL-17A
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.97888, 0.97926, 0.96403	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2	54.665	99.9	0.091	0.091	31.5	26.3	42895	42895	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2	2.11	99.3		0.366	0.366	0.378	0.093	2	15.7	6108

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MAD	2	54.636	42832	37172	4314	99.9	0.223	0.2006	0.2058	0.2394	0.205	random	28.2343

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]
0.081			0.081		-0.163

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_d	1.271
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4757
Nucleic Acid Atoms
Solvent Atoms	537
Heterogen Atoms	2

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
DM	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SOLVE	phasing