3BQ5 | pdb_00003bq5

Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (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
2.23	44.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.229	α = 90
b = 107.164	β = 108.96
c = 107.667	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)	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	47.4	99.8	0.063	15.6	4.8	104606	104398			34.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.12	100		0.398	4.4	4.8	15374

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	47.4	104606	104398	2610	99.8	0.218	0.217	0.21	0.2403	0.24	RANDOM	38.99

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]
1.903		5.615	-4.632		2.729

RMS Deviations
Key	Refinement Restraint Deviation
fIHEDRAL	16.341
fNGLE	0.851
fHIRALITY	0.061
fOND	0.005
fLANARITY	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11230
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms	26

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.