2B4R | pdb_00002b4r

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 Angstrom Resolution reveals intriguing extra electron density in the active site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J0X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	30% PEG 3350; 200 MILLIMOLAR NA F; 100 MILLIMOLAR BIS-TRIS-PROPANE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.327	α = 90
b = 104.585	β = 107.35
c = 90.838	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 315	double crystal monochromator	2005-03-04	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	QUANTUM 315	double crystal monochromator	2005-03-04	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.980699	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.980699	SSRL	BL9-2

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
1,2	2.25	46.37	96.9	0.093	7.4	3.7	54043	54043		-3	49.5

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)
1,2	2.25	2.37	87.1		0.507	2.2	3.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1J0X	2.25	46.37	54043	54043	2892	96.94	0.18587	0.18587	0.18282	0.19	0.2428	0.19	RANDOM	65.472

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]
0.25		0.14	-0.25		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.49
r_dihedral_angle_4_deg	16.043
r_dihedral_angle_3_deg	13.111
r_dihedral_angle_1_deg	5.77
r_scangle_it	2.817
r_scbond_it	1.945
r_mcangle_it	1.753
r_mcbond_it	1.346
r_angle_refined_deg	1.088
r_angle_other_deg	0.715
r_mcbond_other	0.269
r_nbd_refined	0.176
r_nbtor_refined	0.169
r_nbd_other	0.165
r_xyhbond_nbd_refined	0.145
r_symmetry_vdw_other	0.137
r_symmetry_hbond_refined	0.101
r_nbtor_other	0.079
r_symmetry_vdw_refined	0.077
r_chiral_restr	0.059
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10204
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	239

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing