2EIW | pdb_00002eiw

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

X-RAY DIFFRACTION

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, PH5.2; THEN SOAKED IN 30% MPD, 50mM L-proline, 50MM SODIUM Acetate, PH5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.349	α = 90
b = 100.349	β = 90
c = 279.993	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	2006-11-25	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	1.9	25	100	0.069	0.063	24.4	5.7	82759	82759		-3	17.1

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	1.9	1.97	100		0.306	0.277	5.2	5.5	8315

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 (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	1.9	24.61	75124	75124	3970	95.51	0.15868	0.15693	0.16	0.19157	0.19	RANDOM	17.153

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]
1.09	0.55		1.09		-1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.103
r_dihedral_angle_4_deg	16.59
r_dihedral_angle_3_deg	13.632
r_dihedral_angle_1_deg	6.212
r_scangle_it	3.639
r_scbond_it	2.202
r_angle_refined_deg	1.377
r_mcangle_it	1.159
r_mcbond_it	0.665
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.103
r_dihedral_angle_4_deg	16.59
r_dihedral_angle_3_deg	13.632
r_dihedral_angle_1_deg	6.212
r_scangle_it	3.639
r_scbond_it	2.202
r_angle_refined_deg	1.377
r_mcangle_it	1.159
r_mcbond_it	0.665
r_nbtor_refined	0.311
r_metal_ion_refined	0.278
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.183
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8076
Nucleic Acid Atoms
Solvent Atoms	757
Heterogen Atoms	106

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.