2I2X | pdb_00002i2x

Crystal structure of methanol:cobalamin methyltransferase complex MtaBC from Methanosarcina barkeri

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	0.1 M sodium acetate, 0.05 M ammonium sulphate, 17% polyethyleneglycol, 15% glycerole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.75	α = 90
b = 172.85	β = 98.86
c = 190.54	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	CCD	ADSC QUANTUM 4	mirrors	2003-12-09	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MAR CCD 165 mm	mirrors	2003-09-15	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9393	ESRF	ID14-4
2	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.2824	MPG/DESY, HAMBURG	BW6

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	2.5	20	95.3	0.133	9.4	2.6	218403	218403

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	2.5	2.65	89.3		0.445	3.1	2.6	31920

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 (All)	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	SAD	THROUGHOUT	2.5	20	207482	207482	10921	98.54	0.18426	0.18426	0.18179	0.18	0.23146	0.23	RANDOM	37.445

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]
0.78		1.12	-0.9		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.893
r_dihedral_angle_4_deg	21.059
r_dihedral_angle_3_deg	18.556
r_dihedral_angle_1_deg	5.755
r_scangle_it	2.57
r_scbond_it	1.575
r_angle_refined_deg	1.385
r_mcangle_it	1.037
r_mcbond_it	0.549
r_nbtor_refined	0.303
r_metal_ion_refined	0.282
r_symmetry_vdw_refined	0.22
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.133
r_chiral_restr	0.096
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	43880
Nucleic Acid Atoms
Solvent Atoms	946
Heterogen Atoms	740

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XDS	data scaling
SHELXD	phasing