8AZB | pdb_00008azb

Crystal Structure of the peptide binding protein DppE from Bacillus subtilis in the unliganded state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8AY0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Ligand free DppE was crystallised in a sitting drop formed by mixing 150 nl of the unliganded protein at 9 mg.ml-1 with 150 nl of 0.1 M MIB buffer pH 4.0, 25 % (w/v) PEG 1500.

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.53	α = 90
b = 91.08	β = 90
c = 106.74	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		2016-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

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	1.4	46.09	99.6	0.046	0.053	0.026	0.999	20.9	7.4		104801

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	1.4	1.42			0.344	0.436	0.262	0.886		4.4

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	8AY0	1.4	46.089	104711	5232	99.491	0.182	0.1806	0.19	0.2084	0.21	16.093

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]
-0.239			-0.319		0.558

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.407
r_dihedral_angle_3_deg	13.087
r_dihedral_angle_1_deg	6.4
r_dihedral_angle_2_deg	5.791
r_lrange_it	5.46
r_lrange_other	5.279
r_scangle_it	4.219
r_scangle_other	4.218
r_scbond_it	2.888
r_scbond_other	2.883
r_mcangle_other	2.425
r_mcangle_it	2.423
r_angle_refined_deg	1.81
r_mcbond_it	1.657
r_mcbond_other	1.655
r_angle_other_deg	0.593
r_symmetry_xyhbond_nbd_refined	0.34
r_symmetry_nbd_refined	0.243
r_nbd_refined	0.231
r_symmetry_nbd_other	0.189
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.183
r_nbd_other	0.168
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4029
Nucleic Acid Atoms
Solvent Atoms	513
Heterogen Atoms

Software

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