2VFE | pdb_00002vfe

Crystal structure of F96S mutant of Plasmodium falciparum triosephosphate isomerase with 3- phosphoglycerate bound at the dimer interface

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O5X	PDB ENTRY 1O5X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5		0.1 M SODIUM ACETATE PH 4.0 -5.5, PEG 1450 8-24%

Crystal Properties
Matthews coefficient	Solvent content
2.1	43.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.843	α = 90
b = 50.872	β = 92.5
c = 87.067	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	IMAGE PLATE	MARRESEARCH	OSMIC MIRROR	2006-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	2.2	50	97.6	0.09	10.6	2.95		23622			37.9

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	2.2	2.8	87.3		0.42	1.98	2.16

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1O5X	2.2	43.9	22395	1212	97.3	0.22115	0.21833	0.21	0.27563	0.27	RANDOM	34.27

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		-0.11	-0.16		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.188
r_dihedral_angle_3_deg	12.834
r_dihedral_angle_4_deg	8.907
r_dihedral_angle_1_deg	4.607
r_angle_refined_deg	0.893
r_scangle_it	0.599
r_mcangle_it	0.418
r_scbond_it	0.372
r_nbtor_refined	0.289
r_mcbond_it	0.233
r_nbd_refined	0.154
r_symmetry_vdw_refined	0.123
r_xyhbond_nbd_refined	0.106
r_symmetry_hbond_refined	0.079
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3846
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing