3BQ6 | pdb_00003bq6

Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ (Monoclinic)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T7L	PDB ENTRY 1T7L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR BATCH, UNDER OIL	8.5	295	19.5% PEG 3350, 0.2M magnesium acetate, 2.5% ethylene glycol, 0.1M Tris-HCl, pH 8.5, VAPOR BATCH, UNDER OIL, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.087	α = 90
b = 107.604	β = 110.12
c = 107.442	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	MARMOSAIC 300 mm CCD	K-B pair of biomorph mirrors for vertical and horizontal focusing	2006-04-21	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)	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	2.1	48.9	99.9			89790	89746			34.81

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.21	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 1T7L	2.1	48.9	89790	89746	2244	99.9	0.2106	0.2099	0.2	0.2378	0.23	RANDOM	39.12

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]
8.037		-3.953	-7.881		-0.156

RMS Deviations
Key	Refinement Restraint Deviation
fIHEDRAL	15.048
fNGLE	0.845
fHIRALITY	0.056
fOND	0.005
fLANARITY	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11003
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
XDS	data reduction
XSCALE	data scaling
EPMR	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.