2R65 | pdb_00002r65

Crystal structure of Helicobacter pylori ATP dependent protease, FtsH ADP complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IXZ	PDB entry 1IXZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1M MES-NaOH pH 6.5, 17%(w/v) PEG 8000, 0.2M MgSO4, 0.01M ADP, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.471	α = 90
b = 219.485	β = 90
c = 146.692	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	CCD	ADSC QUANTUM 315		2006-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.00	Photon Factory	BL-5A

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	3.3	50	98.4	0.052	0.052	37.9	4.4	25338	25338

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	3.3	3.38	91.9		0.342	0.342	3.2	3.6	1260

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1IXZ	3.3	50	25338	25338	1366	98.62	0.28972	0.28972	0.28762	0.2692	0.33058	0.3119	RANDOM	128.319

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]
-0.41			-8.56		8.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.21
r_dihedral_angle_3_deg	21.728
r_dihedral_angle_4_deg	17.656
r_dihedral_angle_1_deg	6.997
r_mcangle_it	6.263
r_mcbond_it	4.75
r_scangle_it	2.511
r_angle_refined_deg	1.822
r_scbond_it	1.567
r_nbtor_refined	0.318
r_nbd_refined	0.285
r_symmetry_vdw_refined	0.255
r_symmetry_hbond_refined	0.249
r_xyhbond_nbd_refined	0.202
r_chiral_restr	0.112
r_bond_refined_d	0.02
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9510
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	135

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing