1R74

Crystal Structure of Human Glycine N-Methyltransferase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	273	PEG4000, Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.84	α = 90
b = 83.23	β = 90
c = 114.88	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	103	IMAGE PLATE	MARRESEARCH	mirrors	2002-04-02
2	1	x-ray		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.5418

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
2	2.55	12	98.3	0.051	9.9	3.7	23864	23864

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	2.55	2.69	98.3		0.389	1.8	3.6

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1XVA	2.55	12	23864	22070	1623	98.37	0.2249	0.22492	0.2218	0.26605	RANDOM	29.659

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]
-0.13			0.48		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.843
r_scangle_it	4.003
r_scbond_it	2.588
r_angle_refined_deg	2.167
r_angle_other_deg	1.605
r_mcangle_it	1.568
r_mcbond_it	0.862
r_symmetry_hbond_refined	0.438
r_symmetry_vdw_other	0.345
r_nbd_other	0.252
r_nbd_refined	0.242
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.133
r_symmetry_vdw_refined	0.119
r_nbtor_other	0.1
r_gen_planes_other	0.033
r_bond_refined_d	0.027
r_gen_planes_refined	0.017
r_bond_other_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4240
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
CCP4	data scaling
CNS	phasing