2PBF

Crystal structure of a putative protein-L-isoaspartate O-methyltransferase beta-aspartate methyltransferase (PCMT) from Plasmodium falciparum in complex with S-adenosyl-L-homocysteine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L1N	PDB entry 1L1N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	298	25% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Hepes pH 7.2, 2 mM SAH, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.156	α = 90
b = 75.156	β = 90
c = 77.389	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2007-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	2	50	99.1	0.1	0.074	22	5.3	33234	33234

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	2	2.07	90.7		0.899	0.713	2	4.9

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	PDB entry 1L1N	2	33.81	31337	31337	1673	99.2	0.22644	0.22407	0.26789	RANDOM	36.531

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]
1.46	0.73		1.46		-2.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.433
r_dihedral_angle_4_deg	23.12
r_dihedral_angle_3_deg	16.646
r_dihedral_angle_1_deg	6.484
r_scangle_it	2.87
r_scbond_it	1.906
r_angle_refined_deg	1.503
r_mcangle_it	1.309
r_mcbond_it	0.761
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.243
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.175
r_symmetry_hbond_refined	0.126
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
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	3476
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	52

Software

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