8ARN | pdb_00008arn

Crystal structure of the peptide binding protein, OppA, from Bacillus subtilis in complex with an endogenous tetrapeptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RKM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	Crystals of OppA were obtained from hanging drops composed of 2 microlitres of reservoir solution consisting of 0.1 M MMT, 22.5% PEG 1500 and 2.5% DMSO pH 8.0 and 2 microlitres protein at 18 mg.ml-1 with crystal optimisation following a seeding protocol.

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.52	α = 90
b = 65.89	β = 100.97
c = 153.29	γ = 90

Symmetry
Space Group	C 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		2015-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.82	Diamond	I03

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	1.5	55.025	99.9	0.045	0.059	0.038	0.998	12.6	4.2		158694

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	1.5	1.53			0.723	0.955	0.617	0.609		4.2

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	1RKM	1.5	55.025	158693	7849	99.861	0.179	0.1772	0.19	0.2066	0.21	22.694

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]
-0.661		-0.283	1.266		-0.461

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.093
r_dihedral_angle_6_deg	16.002
r_lrange_other	15.461
r_dihedral_angle_3_deg	13.791
r_dihedral_angle_2_deg	7.4
r_dihedral_angle_1_deg	6.494
r_scangle_it	4.666
r_scangle_other	4.666
r_scbond_it	3.151
r_scbond_other	3.151
r_mcangle_it	2.561
r_mcangle_other	2.561
r_mcbond_it	1.975
r_mcbond_other	1.974
r_angle_refined_deg	1.614
r_angle_other_deg	0.557
r_symmetry_nbd_refined	0.234
r_nbd_refined	0.221
r_symmetry_nbd_other	0.193
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.182
r_nbd_other	0.178
r_symmetry_xyhbond_nbd_refined	0.177
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_xyhbond_nbd_other	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8171
Nucleic Acid Atoms
Solvent Atoms	884
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
DIALS	data reduction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing