3DPQ | pdb_00003dpq

Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form B)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DPO	PDB entry 3dpo

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	2.4 M ammonium sulfate, 100 mM citric acid , pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.712	α = 90
b = 91.653	β = 90
c = 154.797	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	293					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.0	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	19.893	86.7	0.076	0.076	6.7	5.4		27880

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.95	2.06	90.4		0.342	0.342	2.1	5.1	10524

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		THROUGHOUT	PDB entry 3dpo	2.6	8	27432	1354	82.05	0.257	0.254	0.27	0.319	0.27	RANDOM	24.921

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]
-1.69			1.81		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.137
r_dihedral_angle_3_deg	19.769
r_dihedral_angle_4_deg	17.979
r_dihedral_angle_1_deg	7.248
r_scangle_it	5.307
r_mcangle_it	5.055
r_scbond_it	3.782
r_mcbond_it	3.6
r_angle_other_deg	1.971
r_angle_refined_deg	1.824

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.137
r_dihedral_angle_3_deg	19.769
r_dihedral_angle_4_deg	17.979
r_dihedral_angle_1_deg	7.248
r_scangle_it	5.307
r_mcangle_it	5.055
r_scbond_it	3.782
r_mcbond_it	3.6
r_angle_other_deg	1.971
r_angle_refined_deg	1.824
r_mcbond_other	0.988
r_chiral_restr	0.103
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6960
Nucleic Acid Atoms
Solvent Atoms	1466
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

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.