2H1R

Crystal structure of a dimethyladenosine transferase from Plasmodium falciparum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZQ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.1	297	23.5% PEG3350, 0.2M Tri Lithium Citrate, 0.1M Hepes at pH7.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.008	α = 90
b = 82.222	β = 112.04
c = 75.909	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	ADSC QUANTUM 210	Si(111)	2006-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.979	CHESS	A1

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	1.9	50	98.9	0.078	0.078	9.8	5	55385	55385

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)
	1.9	1.93	87.4		0.474	0.474	1.95	2.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ZQ9	1.89	50	52513	52513	2825	98.07	0.20111	0.19843	0.24954	RANDOM	29.872

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]
-1.44		-2.08	1.73		-1.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.782
r_dihedral_angle_4_deg	15.674
r_dihedral_angle_3_deg	14.787
r_dihedral_angle_1_deg	5.662
r_scangle_it	4.449
r_scbond_it	2.942
r_mcangle_it	1.813
r_angle_refined_deg	1.459
r_mcbond_it	1.156
r_nbtor_refined	0.307
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.208
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4398
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling
PHASER	phasing