3G5T | pdb_00003g5t

Crystal structure of trans-aconitate 3-methyltransferase from yeast

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	Protein solution (8 mg/ml MSE Protein, 0.040 M NaCl, 0.00024 M TCEP, 0.001 M SAM, 0.008 M Trans-aconitic acid, 0.0045 M HEPES pH 7.0) mixed in a 1:1 ratio with the Well solution (24% PEG 8000, 2% DMSO, 0.05 M HEPES pH 7.5). Cryoprotected with 23% PEG 8000, 2% DMSO, 0.001 M SAM, 0.0085 M Trans-aconitate, 0.05 M HEPES pH 7.5, 19% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.834	α = 90
b = 91.891	β = 90
c = 104.269	γ = 90

Symmetry
Space Group	P 21 21 21

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		2008-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97886	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.119	50	97.4	0.104	32.628	12.5		134803

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.119	1.16	77.3		0.322	4.464	6.5	10548

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	1.119	34.47	134502	6751	98.176	0.121	0.12	0.2557	0.137	0.2665	RANDOM	12.564

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]
-0.161			0.02		0.142

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.672
r_dihedral_angle_4_deg	21.26
r_sphericity_free	15.644
r_dihedral_angle_3_deg	12.732
r_dihedral_angle_1_deg	7.074
r_sphericity_bonded	6.338
r_scangle_it	5.801
r_scbond_it	4.455
r_mcangle_it	3.212
r_rigid_bond_restr	2.402
r_mcbond_it	2.263
r_angle_refined_deg	2.262
r_mcbond_other	1.103
r_angle_other_deg	0.88
r_chiral_restr	0.154
r_bond_refined_d	0.03
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4891
Nucleic Acid Atoms
Solvent Atoms	541
Heterogen Atoms	75

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling