4M3P | pdb_00004m3p

Betaine-Homocysteine S-Methyltransferase from Homo sapiens complexed with Homocysteine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LT8	PDB ENTRY 1LT8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.5	277	20.0% PEG5000 MME, 0.2 M sodium/potassium tartrate, 1.4% 1,2,3-heptanetriol, pH 7.5, EVAPORATION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.097	α = 90
b = 102.617	β = 101.76
c = 96.228	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	2006-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	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	1.895	45.222	98.2	0.083	0.072	13.7	4.1	129862	128582			34.8

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	1.895	2.01	90		0.374	0.369	4	4.1	19787

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 1LT8	1.895	45.222	123327	122106	6476	99.01	0.18214	0.18021	0.19	0.21852	0.22	RANDOM	33.943

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]
-0.14		0.42	2.05		-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.218
r_dihedral_angle_4_deg	17.951
r_dihedral_angle_3_deg	15.009
r_dihedral_angle_1_deg	5.516
r_angle_refined_deg	1.356
r_angle_other_deg	0.806
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.218
r_dihedral_angle_4_deg	17.951
r_dihedral_angle_3_deg	15.009
r_dihedral_angle_1_deg	5.516
r_angle_refined_deg	1.356
r_angle_other_deg	0.806
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11469
Nucleic Acid Atoms
Solvent Atoms	644
Heterogen Atoms	60

Software

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

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.