2CBY

Crystal structure of the ATP-dependent Clp Protease proteolytic subunit 1 (ClpP1) from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TYF	PDB ENTRY 1TYF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8		THE PROTEIN WAS CRYSTALLISED BY THE VAPOUR DIFFUSION METHOD IN HANGING DROPS CONTAINING A 1:1 MIXTURE OF 3 MG/ML PROTEIN SOLUTION (IN 50 MM TRIS-HCL PH 8) AND RESERVOIR SOLUTION INCLUDING 1 M AMMONIUM SULPHATE IN 0.1 M HEPES PH 8.

Crystal Properties
Matthews coefficient	Solvent content
3.83	67.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.255	α = 90
b = 178.255	β = 90
c = 264.914	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	110	CCD	MARRESEARCH		2001-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.6	76.7	100	0.16	24.3	22.2		76728			40.12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.74	100		0.69	6.6	22.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1TYF	2.6	154.3	76647	3895	100	0.194	0.192	0.19	0.229	0.22	RANDOM	19.59

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]
0.872	0.436		0.872		-1.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.912
r_dihedral_angle_3_deg	19.468
r_dihedral_angle_4_deg	18.233
r_dihedral_angle_1_deg	6.21
r_scangle_it	3.798
r_scbond_it	2.318
r_angle_refined_deg	1.48
r_mcangle_it	1.333
r_mcbond_it	0.805
r_nbtor_refined	0.313
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.193
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9149
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing