4RYF | pdb_00004ryf

ClpP1/2 heterocomplex from Listeria monocytogenes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JCQ	4JCQ, 4JCT
experimental model	PDB	4JCT	4JCQ, 4JCT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.2 M Sodium-Malonate, 40% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.23	α = 90
b = 127.15	β = 90
c = 265.5	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	100	PIXEL	PSI PILATUS 6M		2014-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	2.8	30	96.2	0.096	14.2	4.7	81904	78792	2	2

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	2.8	2.9	98.1		0.48	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	4JCQ, 4JCT	2.8	30	2	78758	74817	3941	96.21	0.18144	0.17962	0.18	0.21573	0.22	RANDOM	47.426

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]
-1.03			0.29		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.954
r_sphericity_free	31.771
r_sphericity_bonded	20.632
r_dihedral_angle_4_deg	20.581
r_dihedral_angle_3_deg	18.353
r_dihedral_angle_1_deg	5.024
r_long_range_B_refined	3.333
r_scbond_it	2.53
r_mcangle_it	2.473
r_mcbond_it	1.93
r_angle_refined_deg	0.919
r_rigid_bond_restr	0.796
r_chiral_restr	0.066
r_bond_refined_d	0.004
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19674
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	63

Software

Software
Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling