3DRF | pdb_00003drf

Lactococcal OppA complexed with an endogenous peptide in the closed conformation

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.2M NaCl, 0.1M Na-Hepes, pH 7.0, 20% PEG 6000, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	36.430637

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.114	α = 90
b = 74.65	β = 90
c = 115.445	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	CCD	ADSC Q210r		2007-02-18	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC Q315R		2007-02-18	M	MAD
3	1	x-ray	100	CCD	ADSC Q315R		2007-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	0.999	ESRF	BM16
2	SYNCHROTRON	ESRF BEAMLINE ID29	0.9197, 0.9199, 0.9168	ESRF	ID29
3	SYNCHROTRON	ESRF BEAMLINE ID29	1.775	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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
1,2,3	1.3		99.4	0.053	19.61			124464		-3	14.587

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3	1.3	1.38	97.9		0.364	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MAD	THROUGHOUT	1.3	62.75	119254	6300	99.64	0.13286	0.13132	0.14	0.16147	0.17	RANDOM	8.442

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]
0.03			-0.2		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.259
r_dihedral_angle_4_deg	16.57
r_dihedral_angle_3_deg	10.93
r_dihedral_angle_1_deg	6.597
r_sphericity_free	4.051
r_scangle_it	3.074
r_scbond_it	2.051
r_sphericity_bonded	1.803
r_mcangle_it	1.381
r_angle_refined_deg	1.29
r_rigid_bond_restr	0.879
r_angle_other_deg	0.859
r_mcbond_it	0.859
r_mcbond_other	0.339
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4249
Nucleic Acid Atoms
Solvent Atoms	1119
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHARP	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction