6TMU | pdb_00006tmu

Crystal structure of the chaperonin gp146 from the bacteriophage EL 2 (Pseudomonas aeruginosa) in presence of ATP-BeFx, crystal form II

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WF4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	293	8 % PEG-6000, 0.15 M NaCl and 0.1 M Tris-HCl pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.516	α = 90
b = 151.461	β = 90
c = 261.347	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	DECTRIS PILATUS 6M		2018-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.8500	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.54	49.47	99.8	0.111	0.125	0.056	0.997	7.9	4.9		70880

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.54	3.62	99.9		1.119	1.255	0.557	0.465		4.9

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	EMD-6492	3.54	30	67159	3576	99.51	0.2516	0.2504	0.24	0.2747	0.27	RANDOM	170.101

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]
0.38			1.36		-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.559
r_dihedral_angle_3_deg	13.241
r_dihedral_angle_4_deg	10.922
r_dihedral_angle_1_deg	5.054
r_angle_refined_deg	0.967
r_angle_other_deg	0.865
r_chiral_restr	0.051
r_bond_refined_d	0.005
r_bond_other_d	0.003
r_gen_planes_refined	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.559
r_dihedral_angle_3_deg	13.241
r_dihedral_angle_4_deg	10.922
r_dihedral_angle_1_deg	5.054
r_angle_refined_deg	0.967
r_angle_other_deg	0.865
r_chiral_restr	0.051
r_bond_refined_d	0.005
r_bond_other_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	29093
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	213

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.