8AY0 | pdb_00008ay0

Crystal Structure of the peptide binding protein DppE from Bacillus subtilis in complex with murein tripeptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FAJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	Crystals of DppE suitable for X-ray analysis were obtained from hanging drops formed by mixing 1 mircol of reservoir solution containing 0.1 M Bis-Tris-Propane pH 8.5, 0.4 M MgCl2, 22.5 % PEG 3350 and 2.5 % DMSO with 1 microl of protein at 13 mg.ml-1 .

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.855	α = 78.088
b = 61.31	β = 82.672
c = 124.073	γ = 61.597

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	PIXEL	DECTRIS PILATUS 6M		2015-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.51	60.74	96.3	0.053	0.075	0.053	0.998	8.4	2.2		233391

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	1.51	1.54			0.759	1.073	0.759	0.572		2.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4FAJ	1.51	60.739	233390	11490	96.293	0.186	0.1845	0.19	0.2213	0.23	24.662

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]
-0.88	-0.029	1.355	0.324	-2.004	-0.326

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.169
r_dihedral_angle_3_deg	14.104
r_dihedral_angle_1_deg	6.697
r_dihedral_angle_2_deg	5.743
r_lrange_it	5.686
r_lrange_other	5.685
r_scangle_it	4.24
r_scangle_other	4.24
r_scbond_it	2.86
r_scbond_other	2.86
r_mcangle_it	2.835
r_mcangle_other	2.835
r_mcbond_it	2.073
r_mcbond_other	2.072
r_angle_refined_deg	1.502
r_angle_other_deg	0.522
r_symmetry_xyhbond_nbd_refined	0.278
r_nbd_refined	0.223
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.181
r_nbd_other	0.179
r_symmetry_nbd_refined	0.168
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.044
r_metal_ion_refined	0.024
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_xyhbond_nbd_other	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11876
Nucleic Acid Atoms
Solvent Atoms	1206
Heterogen Atoms	177

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
MOLREP	phasing