2EHQ | pdb_00002ehq

Crystal analysis of 1-pyrroline-5-carboxylate dehydrogenase from thermus with bound NADP

X-RAY DIFFRACTION

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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, PH 5.2; THEN SOAKED IN 30% MPD, 5mM NADP, 50MM SODIUM Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.426	α = 90
b = 102.426	β = 90
c = 278.837	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		2006-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	1.0	SPring-8	BL44XU

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	1.55	25	100	0.06	0.055	30.9	5.7	158273	158273		-3	12.9

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	1.55	1.59	100		0.435	0.4	4.2	5.6	10482

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 2bhp	1.55	22.11	150390	145352	7695	96.65	0.15917	0.15804	0.1573	0.18039	0.1788	RANDOM	12.393

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]
0.38	0.19		0.38		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.279
r_dihedral_angle_4_deg	14.76
r_dihedral_angle_3_deg	11.908
r_dihedral_angle_1_deg	6.105
r_scangle_it	2.85
r_scbond_it	1.688
r_angle_refined_deg	1.238
r_mcangle_it	0.925
r_mcbond_it	0.488
r_nbtor_refined	0.311
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.174
r_metal_ion_refined	0.157
r_symmetry_hbond_refined	0.108
r_xyhbond_nbd_refined	0.1
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8076
Nucleic Acid Atoms
Solvent Atoms	1042
Heterogen Atoms	170

Software

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