1X7P | pdb_00001x7p

Crystal structure of the SpoU Methyltransferase AviRb from Streptomyces viridochromogenes in complex with the cofactor AdoMet

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.8	293	PEG 300, MES, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.881	α = 90
b = 76.881	β = 90
c = 209.818	γ = 90

Symmetry
Space Group	P 41 21 2

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	MARRESEARCH		2003-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9762	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.55	25	100	0.064	0.076	18.8	9.4		21375	2	2	55.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.68	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	2.55	25	20283	20283	1067	100	0.20477	0.202	0.21	0.25653	0.25	RANDOM	25.26

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]
-0.12			-0.12		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.866
r_scangle_it	2.312
r_angle_refined_deg	1.426
r_scbond_it	1.315
r_angle_other_deg	0.86
r_mcangle_it	0.857
r_mcbond_it	0.452
r_symmetry_vdw_other	0.231
r_nbd_other	0.22
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.186
r_symmetry_vdw_refined	0.182
r_symmetry_hbond_refined	0.135
r_nbtor_other	0.085
r_chiral_restr	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3955
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing