2EJL | pdb_00002ejl

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

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.04	α = 90
b = 102.04	β = 90
c = 279.352	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	1.5	25	100	0.054	0.048	32.9	5.6	173614	173614		-3	13.1

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	1.5	1.53	100		0.456	0.407	3.8	5.4	11553

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 2bhp	1.5	25	156770	156770	8278	95.02	0.18356	0.18356	0.18244	0.18	0.20465	0.2	RANDOM	12.548

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]
0.37	0.19		0.37		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.134
r_dihedral_angle_4_deg	14.552
r_dihedral_angle_3_deg	12.459
r_dihedral_angle_1_deg	10.759
r_scangle_it	2.85
r_scbond_it	1.721
r_angle_refined_deg	1.216
r_mcangle_it	0.958
r_mcbond_it	0.539
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.134
r_dihedral_angle_4_deg	14.552
r_dihedral_angle_3_deg	12.459
r_dihedral_angle_1_deg	10.759
r_scangle_it	2.85
r_scbond_it	1.721
r_angle_refined_deg	1.216
r_mcangle_it	0.958
r_mcbond_it	0.539
r_nbtor_refined	0.311
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.176
r_metal_ion_refined	0.127
r_xyhbond_nbd_refined	0.117
r_symmetry_hbond_refined	0.116
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8078
Nucleic Acid Atoms
Solvent Atoms	985
Heterogen Atoms	128

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.