5GKM

Crystal structure of the N-terminal Domain of Caseinolytic protease associated chaperone ClpD from Arabidopsis thaliana

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CTZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	291	20%(v/v) 2-propanol, 20%(w/v) PEG MME 2000, 100 mM MES monohydrate

Crystal Properties
Matthews coefficient	Solvent content
2	38.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.08	α = 90
b = 37.31	β = 96.08
c = 99.98	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD		2016-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9537	ESRF	BM14

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	1.6	50	100	0.065	0.995	9.8	4.2		37033

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	1.6	1.63	100		0.583	0.717	2	4.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5CTZ	1.6	35	35497	1771	100	0.197	0.196	0.212	RANDOM	23.11

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]
0.33		0.05	0.34		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.456
r_dihedral_angle_4_deg	22.165
r_dihedral_angle_3_deg	12.341
r_dihedral_angle_1_deg	5.749
r_long_range_B_refined	4.851
r_long_range_B_other	4.835
r_scangle_other	4.089
r_scbond_it	2.961
r_scbond_other	2.96
r_mcangle_it	2.042
r_mcangle_other	2.041
r_angle_refined_deg	1.706
r_mcbond_it	1.584
r_mcbond_other	1.579
r_angle_other_deg	0.886
r_chiral_restr	0.118
r_bond_refined_d	0.018
r_gen_planes_refined	0.016
r_bond_other_d	0.006
r_gen_planes_other	0.003
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	2301
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms

Software

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