4DJM | pdb_00004djm

Crystal structure of the E. coli chaperone DraB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CO6	PDB ENTRY 2CO6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	protein solution: 15 mg/ml protein, 20 mM Tris pH 8.0, 200 mM NaCl, 10 % glycerol well solution: 200 mM MgCl2, 100 mM Bis-Tris pH 6.5, 25% PEG3350 protein and well solutions mixed 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.45	α = 84.2
b = 98.41	β = 89.8
c = 100.88	γ = 83.8

Symmetry
Space Group	P 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 300 mm CCD	mirrors	2009-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.9724	APS	23-ID-D

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	2.5	30	98.4	0.109	0.109	13.4	3.9	76049	74832	-3	-3	51.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 2CO6	2.52	30	73265	73265	1489	100	0.20709	0.20709	0.20581	0.21	0.26871	0.26	RANDOM	47.597

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]
2	-0.12	0.87	1.21	-0.67	-3.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.576
r_dihedral_angle_3_deg	22.804
r_dihedral_angle_4_deg	19.963
r_scangle_it	9.264
r_dihedral_angle_1_deg	7.974
r_scbond_it	6.855
r_mcangle_it	4.673
r_mcbond_it	2.732
r_angle_refined_deg	2.151
r_chiral_restr	0.148

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.576
r_dihedral_angle_3_deg	22.804
r_dihedral_angle_4_deg	19.963
r_scangle_it	9.264
r_dihedral_angle_1_deg	7.974
r_scbond_it	6.855
r_mcangle_it	4.673
r_mcbond_it	2.732
r_angle_refined_deg	2.151
r_chiral_restr	0.148
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12557
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.