2EJD | pdb_00002ejd

Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound L-alanine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BHQ	PDB ENTRY 2bhq

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.2	293	30% MPD, 50MM SODIUM CITRATE/HCL, 50mM L-alanine, 50 MM SODIUM Acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.661	α = 90
b = 101.661	β = 90
c = 279.261	γ = 120

Symmetry
Space Group	H 3

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	mirrors	2006-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	1.0	SPring-8	BL44B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.85	25	99.2	0.086	0.075	16.3	4.3	91379	91379		-3	15.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.92	97.8		0.448	0.391	2.9	3.9	8962

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2bhq	1.85	24.51	83883	83883	4426	95.87	0.15533	0.15533	0.15346	0.1523	0.18994	0.1882	RANDOM	16.448

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]
0.01	0.01		0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.093
r_dihedral_angle_4_deg	16.987
r_dihedral_angle_3_deg	13.162
r_dihedral_angle_1_deg	11.547
r_scangle_it	3.664
r_scbond_it	2.186
r_angle_refined_deg	1.328
r_mcangle_it	1.122
r_mcbond_it	0.636
r_nbtor_refined	0.311
r_metal_ion_refined	0.261
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.185
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8078
Nucleic Acid Atoms
Solvent Atoms	860
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing