2NV0 | pdb_00002nv0

Structure of the glutaminase subunit Pdx2 (YaaE) of PLP synthase from Bacillus subtilis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	298	12.4% PEG 8000, 6% ethylene glycol, 100mM cacodylic acid, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.44	α = 90
b = 81.606	β = 90
c = 117.285	γ = 90

Symmetry
Space Group	P 21 21 21

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 4	ESRF	2005-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9340	ESRF	ID14-1

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	1.73	50	98.4	0.065	17.3	5.3	46456	45697			28

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	1.73	1.75	99.9		0.492	2	3.9

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1R9G	1.73	50	43316	2310	98.37	0.18147	0.17956	0.19	0.21579	0.23	RANDOM	29.489

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]
-0.84			1.19		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.867
r_dihedral_angle_4_deg	19.338
r_dihedral_angle_3_deg	14.578
r_dihedral_angle_1_deg	5.761
r_scangle_it	4.556
r_scbond_it	3.017
r_mcangle_it	2.093
r_angle_other_deg	2.007
r_mcbond_it	1.712
r_angle_refined_deg	1.706
r_symmetry_vdw_other	0.363
r_symmetry_vdw_refined	0.36
r_xyhbond_nbd_refined	0.296
r_nbd_refined	0.249
r_nbd_other	0.239
r_mcbond_other	0.188
r_symmetry_hbond_refined	0.183
r_nbtor_refined	0.181
r_chiral_restr	0.108
r_nbtor_other	0.085
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.002
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	2892
Nucleic Acid Atoms
Solvent Atoms	405
Heterogen Atoms

Software

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