3BOL | pdb_00003bol

Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	25% 1,2-propanediol, 10% glycerol, 5% PEG 3000, 100 mM potasium citrate pH 4.8, 1.5% 1,2,3-heptanetriol, 10 mM YCl3. Soaking with 20% 1,2-propanediol, 10% glycerol, 5% PEG 3000, 100 mM TRIS pH 7, and 1.5% 1,2,3-heptanetriol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.626	α = 90
b = 85.841	β = 100.67
c = 125.587	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		CCD	MARMOSAIC 300 mm CCD	K-B pair of biomorph mirrors for vertical and horizontal focusing	2007-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.9793	APS	23-ID-D

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	1.85	47.62	100	0.057	0.062	21.65	7.5	106175	106165			31.916

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.85	1.96	100		0.267	0.417	5.6	7.5	16806

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	1.85	47.62	106175	106164	5351	99.99	0.195	0.193	0.19	0.228	0.23	RANDOM	29.964

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]
1.07		0.34	0.54		-1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.829
r_dihedral_angle_4_deg	19.707
r_dihedral_angle_3_deg	14.53
r_dihedral_angle_1_deg	6.084
r_scangle_it	4.733
r_scbond_it	2.823
r_mcangle_it	1.81
r_angle_refined_deg	1.53
r_mcbond_it	0.984
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.219
r_symmetry_hbond_refined	0.214
r_xyhbond_nbd_refined	0.133
r_symmetry_metal_ion_refined	0.133
r_chiral_restr	0.11
r_metal_ion_refined	0.11
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8687
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	14

Software

Software
Software Name	Purpose
XSCALE	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
CNS	refinement