2EII

Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound L-valine and NAD.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J40

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.2	293	30% MPD, 50MM SODIUM CITRATE/HCL, 5mM NAD+, 50mM L-valine, 100MM SODIUM Acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.208	α = 90
b = 102.208	β = 90
c = 278.432	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	RIGAKU JUPITER 210	mirrors	2006-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0	SPring-8	BL26B1

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	1.88	92.85	99.4	0.037	0.03	33.9	3.5	87940	87940		-3	16

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	1.88	1.95	99.4		0.108	0.087	7.5	3.1	8818

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2j40	1.88	50	83526	83526	4410	99.42	0.13556	0.13556	0.13385	0.16812	RANDOM	15.511

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]
0.76	0.38		0.76		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.089
r_dihedral_angle_4_deg	16.274
r_dihedral_angle_3_deg	12.66
r_dihedral_angle_1_deg	6.255
r_scangle_it	3.386
r_scbond_it	1.981
r_angle_refined_deg	1.295
r_mcangle_it	1.068
r_mcbond_it	0.561
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.089
r_dihedral_angle_4_deg	16.274
r_dihedral_angle_3_deg	12.66
r_dihedral_angle_1_deg	6.255
r_scangle_it	3.386
r_scbond_it	1.981
r_angle_refined_deg	1.295
r_mcangle_it	1.068
r_mcbond_it	0.561
r_nbtor_refined	0.311
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.175
r_symmetry_hbond_refined	0.139
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.089
r_metal_ion_refined	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8076
Nucleic Acid Atoms
Solvent Atoms	976
Heterogen Atoms	234

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.