2J40 | pdb_00002j40

1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound inhibitor L-proline and NAD.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.2		PROTEIN WAS CRYSTALLIZED FROM 37.5% MRD, 50 MM SODIUM CITRATE, PH 5.2; THEN SOAKED IN 2MM NAD, 100MM L-PROLINE, 50 MM SODIUM ACETATE PH5.2.

Crystal Properties
Matthews coefficient	Solvent content
2.4	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.043	α = 90
b = 102.043	β = 90
c = 278.6	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 CCD	MIRRORS	2006-05-24	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	30	99.7	0.1	11.1	3.2		62989		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	98.9		0.32	2	2.7

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2BJK	2.1	30	59782	3193	99.7	0.142	0.14	0.14	0.189	RANDOM	19.21

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]
1.32	0.66		1.32		-1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.976
r_dihedral_angle_4_deg	18.366
r_dihedral_angle_3_deg	13.903
r_dihedral_angle_1_deg	9.954
r_scangle_it	3.939
r_scbond_it	2.455
r_angle_refined_deg	1.536
r_mcangle_it	1.275
r_mcbond_it	0.707
r_nbtor_refined	0.308
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.137
r_symmetry_hbond_refined	0.128
r_chiral_restr	0.103
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8078
Nucleic Acid Atoms
Solvent Atoms	788
Heterogen Atoms	170

Software

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