3WDE | pdb_00003wde

Mutant N-terminal domain of Mycobacterium tuberculosis ClpC1, F80Y, bound to Cyclomarin A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WDC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.2M ammonium acetate, 20% polyethylene glycol 3350, 0.025M magnesium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.76	30.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.02	α = 90
b = 58.86	β = 90
c = 63.99	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	PSI PILATUS 6M		2011-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	SLS	X10SA

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	1.44	50					23876

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	3WDC	1.44	30	22599	1217	99.45	0.1293	0.1267	0.12	0.1767	0.17	RANDOM	13.8438

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]
-0.58			0.01		0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	40.028
r_dihedral_angle_2_deg	38.601
r_dihedral_angle_4_deg	18.606
r_sphericity_bonded	16.151
r_dihedral_angle_3_deg	13.892
r_dihedral_angle_1_deg	4.655
r_rigid_bond_restr	2.549
r_angle_refined_deg	1.818
r_chiral_restr	0.101
r_bond_refined_d	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	40.028
r_dihedral_angle_2_deg	38.601
r_dihedral_angle_4_deg	18.606
r_sphericity_bonded	16.151
r_dihedral_angle_3_deg	13.892
r_dihedral_angle_1_deg	4.655
r_rigid_bond_restr	2.549
r_angle_refined_deg	1.818
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1218
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	4

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.