5OQZ | pdb_00005oqz

Crystal structure of the lasso peptide rubrivinodin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291.15	0.7 M sodium acetate pH 4.6, 30%(v/v) glycerol, 4.6%(w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.45	15.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 15.034	α = 90
b = 27.243	β = 116.76
c = 15.174	γ = 90

Symmetry
Space Group	P 1 21 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		2013-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.799905	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	0.8	50	81.8	1	35.85	3		9545

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	AB INITIO PHASING	THROUGHOUT	0.806	13.622	9038	470	83.71	0.0848	0.0844	0.0856	0.0913	0.0907	RANDOM	3.933

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]
-0.06		-0.08	0.05		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.758
r_dihedral_angle_4_deg	14.941
r_dihedral_angle_3_deg	12.362
r_sphericity_free	11.269
r_dihedral_angle_1_deg	7.534
r_sphericity_bonded	3.984
r_angle_refined_deg	2.147
r_rigid_bond_restr	1.516
r_angle_other_deg	1.105
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	134
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XPREP	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXDE	phasing