3ST9 | pdb_00003st9

Crystal structure of ClpP in heptameric form from Staphylococcus aureus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	295	100mM citric acid, 2.0M ammonium sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.289	α = 90
b = 121.289	β = 90
c = 404.377	γ = 120

Symmetry
Space Group	P 61 2 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	CCD	MARMOSAIC 225 mm CCD		2010-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9795	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.43	50	98.9			68192	67444	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.43	2.52	91.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.43	20	2.6	63748	63145	3364	99.07	0.2405	0.2389	0.27139	0.2767	RANDOM	56.47

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]
1.34	0.67		1.34		-2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.449
r_dihedral_angle_3_deg	16.667
r_dihedral_angle_4_deg	14.495
r_dihedral_angle_1_deg	4.888
r_scangle_it	1.394
r_angle_refined_deg	0.952
r_scbond_it	0.841
r_mcangle_it	0.782
r_mcbond_it	0.444
r_nbtor_refined	0.294
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.13
r_symmetry_hbond_refined	0.123
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9294
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	17

Software

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