8ARE | pdb_00008are

Crystal structure of the peptide binding protein, OppA, from Bacillus subtilis in complex with a PhrE-derived pentapeptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		OppA-SNSS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	291	Crystals of BsOppA in complex with Ser-Arg-Asn-Val-Thr where grown from the products of an isothermal titration calorimetry experiment. This recovered material was fed into a crystallisation screening experiment in MRC-Wilden 96 well plates. A single crystal of BsOppA-SRNVT was grown from 0.1 M SPG (succinic acid, sodium dihydrogen phosphate, glycine) 25% (w/v) PEG 1500 pH 4.0,

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.861	α = 90
b = 63.689	β = 114.352
c = 100.06	γ = 90

Symmetry
Space Group	I 1 2 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-F		2018-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	1.9	52.263	100	0.233	0.313	0.206	0.955	3.2	4.1		37997

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	1.9	1.94			1.056	1.415	0.933	0.758		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	OppA-SNSS	1.9	52.263	37789	1811	99.372	0.255	0.2518	0.2506	0.3084	0.3096	15.642

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]
1.48		-1.011	1.549		-1.499

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.821
r_dihedral_angle_3_deg	15.394
r_dihedral_angle_2_deg	7.198
r_dihedral_angle_1_deg	7.084
r_lrange_it	3.171
r_lrange_other	3.099
r_scangle_it	2.079
r_scangle_other	2.074
r_mcangle_it	1.67
r_mcangle_other	1.67
r_angle_refined_deg	1.391
r_scbond_it	1.315
r_scbond_other	1.301
r_mcbond_it	1.056
r_mcbond_other	1.056
r_angle_other_deg	0.478
r_symmetry_nbd_refined	0.257
r_nbd_refined	0.218
r_nbd_other	0.218
r_symmetry_nbd_other	0.196
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.169
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.041
r_bond_refined_d	0.007
r_gen_planes_refined	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	4060
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	5

Software

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