2ABW | pdb_00002abw

Glutaminase subunit of the plasmodial PLP synthase (Vitamin B6 biosynthesis)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R9G	1R9G CHAIN A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	292	30% PEG200, 5% PEG8000 buffered with 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2	39.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.042	α = 90
b = 67.917	β = 92.31
c = 70.327	γ = 90

Symmetry
Space Group	C 1 2 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		2004-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9791	ESRF	ID29

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	1.62	25	99.9	0.064	19.25	5.2	52687	52658	20	-4

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	1.62	1.63	100	100	0.466	2.25	4.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1R9G CHAIN A	1.62	25	52656	2676	99.941	0.153	0.153	0.1515	0.16	0.1892	0.2	19.129

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]
0.214		-0.161	0.309		-0.536

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.325
r_dihedral_angle_4_deg	16.78
r_dihedral_angle_3_deg	13.705
r_dihedral_angle_1_deg	6.943
r_scangle_it	4.421
r_scbond_it	3.584
r_scangle_other	2.258
r_mcangle_it	2.179
r_mcbond_it	2.029
r_angle_refined_deg	1.962
r_scbond_other	1.333
r_angle_other_deg	1.056
r_mcangle_other	1.024
r_mcbond_other	0.385
r_nbd_refined	0.279
r_symmetry_hbond_refined	0.262
r_symmetry_vdw_other	0.234
r_xyhbond_nbd_refined	0.228
r_nbd_other	0.226
r_symmetry_vdw_refined	0.223
r_nbtor_refined	0.188
r_chiral_restr	0.127
r_nbtor_other	0.089
r_bond_refined_d	0.023
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3483
Nucleic Acid Atoms
Solvent Atoms	469
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction