5KWA | pdb_00005kwa

complete structure of the Mycobacterium tuberculosis proteasomal ATPase Mpa

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M9B	3M9B, 3WHK
experimental model	PDB	3WHK	3M9B, 3WHK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	288	100mM Tris-HCl, 20%PEG400, 200mM MgCl2, 5mM ATPrS

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.931	α = 90
b = 111.931	β = 90
c = 196.072	γ = 120

Symmetry
Space Group	P 3 2 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 315r		2013-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9791	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.9	43.45	100	0.112	0.984	7	10.6		32237			56.52

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.06	100		0.703	0.506		10.5

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	3M9B, 3WHK	2.9	43.45	30678	1543	99.89	0.22974	0.22786	0.23	0.26883	0.27	RANDOM	61.887

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]
-1.49	-0.75		-1.49		4.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.032
r_dihedral_angle_3_deg	16.497
r_dihedral_angle_4_deg	14.204
r_long_range_B_refined	6.551
r_long_range_B_other	6.551
r_dihedral_angle_1_deg	6.044
r_mcangle_it	3.992
r_mcangle_other	3.992
r_scangle_other	3.876
r_mcbond_it	2.305
r_mcbond_other	2.303
r_scbond_it	2.192
r_scbond_other	2.189
r_angle_refined_deg	1.309
r_angle_other_deg	0.926
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7102
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing