2B4T | pdb_00002b4t

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	pdb entry 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 = 69.687	α = 90
b = 106.056	β = 107.24
c = 91.057	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	2005-03-04	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	QUANTUM 315	double crystal	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	0.9807	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9807	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	2.5	46.625	98	0.101	7.9	3.5	42843	42843		-3	68.4

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	2.5	2.64	97.8		0.484	2.2	3.6	6197

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	pdb entry 1J0X	2.5	43.48	40675	40675	2147	97.69	0.17575	0.17575	0.17352	0.19	0.21677	0.19	RANDOM	48.808

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]
4.22		1.59	-1.07		-2.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.973
r_dihedral_angle_4_deg	16.91
r_dihedral_angle_3_deg	13.659
r_dihedral_angle_1_deg	5.693
r_scangle_it	2.797
r_scbond_it	1.924
r_mcangle_it	1.647
r_mcbond_it	1.257
r_angle_refined_deg	1.08
r_angle_other_deg	0.712
r_symmetry_hbond_refined	0.283
r_mcbond_other	0.249
r_symmetry_vdw_refined	0.236
r_nbd_refined	0.187
r_symmetry_vdw_other	0.184
r_nbtor_refined	0.173
r_nbd_other	0.169
r_xyhbond_nbd_refined	0.15
r_nbtor_other	0.08
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	10184
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	215

Software

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