2WBO

Crystal structure of VioC in complex with L-arginine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OG5	PDB ENTRY 2OG5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		1.2 M K-/NA-TARTRATE 0.1 M TRIS/HCL PH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.63	α = 90
b = 67.34	β = 108.83
c = 62.42	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	MIRRORS	2007-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	1.3	20	98.3	0.08	10.1	4.3		76258		-3

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	1.3	1.33	90.2		0.63	2.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2OG5	1.3	59.03	74865	1398	98.3	0.162	0.161	0.212	RANDOM	17.52

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]
-0.2		-1.45	-0.52		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.74
r_dihedral_angle_4_deg	17.053
r_dihedral_angle_3_deg	13.33
r_dihedral_angle_1_deg	7.542
r_scangle_it	7.095
r_mcangle_it	5.759
r_scbond_it	5.613
r_mcbond_it	5.098
r_angle_refined_deg	1.129
r_angle_other_deg	0.879
r_symmetry_vdw_other	0.279
r_nbd_refined	0.205
r_nbd_other	0.205
r_symmetry_hbond_refined	0.187
r_nbtor_refined	0.171
r_symmetry_vdw_refined	0.143
r_xyhbond_nbd_refined	0.13
r_nbtor_other	0.082
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2608
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing