4DT4 | pdb_00004dt4

Crystal structure of the PPIase-chaperone SlpA with the chaperone binding site occupied by the linker of the purification tag

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	28% PEG 3350, 6% MPD (2-methyl-2,4-pentane diol), 100 mM MgCl2 and 100 mM Bis-Tris pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.12	α = 90
b = 29.23	β = 93.2
c = 60.69	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	ADSC QUANTUM 315r		2011-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.93927	ESRF	ID14-4

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	1.35	50	95.5		3.9		29909	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.43	93.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	1.35	34.31	2	29909	1200	95.52	0.16126	0.15956	0.17	0.20107	0.21	RANDOM	17.577

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]
0.41		0.04	0.74		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.273
r_dihedral_angle_3_deg	11.966
r_dihedral_angle_4_deg	9.062
r_scangle_it	8.289
r_dihedral_angle_1_deg	6.194
r_scbond_it	5.887
r_mcangle_it	4.18
r_rigid_bond_restr	3.228
r_mcbond_it	2.874
r_angle_refined_deg	2.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.273
r_dihedral_angle_3_deg	11.966
r_dihedral_angle_4_deg	9.062
r_scangle_it	8.289
r_dihedral_angle_1_deg	6.194
r_scbond_it	5.887
r_mcangle_it	4.18
r_rigid_bond_restr	3.228
r_mcbond_it	2.874
r_angle_refined_deg	2.297
r_chiral_restr	0.146
r_bond_refined_d	0.027
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1209
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms

Software

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