2FZN | pdb_00002fzn

Structure of the E. coli PutA proline dehydrogenase domain reduced by dithionite and complexed with proline

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TJ0	PDB Entry: 1TJ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7	293	The crystal was grown in 13-15% PEG 3350, 60-190 mM citrate buffer. Prior to data collection a crystal was soaked in excess Na dithionite and proline in order to reduce the FAD cofactor., pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.115	α = 90
b = 143.221	β = 90
c = 145.124	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	173	CCD	ADSC QUANTUM 4		2003-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97856	APS	19-ID

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	27	98.1	0.061	12.3	5.7		51335

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	2.07		91.2	0.419		4.7

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry: 1TJ0	2	22.7	49878	2508	100	0.216	0.216	0.214	0.22	0.251	0.26	RANDOM	25.509

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]
-0.77			4.87		-4.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.425
r_scangle_it	3.458
r_scbond_it	2.157
r_angle_refined_deg	1.413
r_mcangle_it	1.32
r_angle_other_deg	0.834
r_mcbond_it	0.733
r_symmetry_vdw_other	0.257
r_nbd_other	0.243
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.152
r_symmetry_vdw_refined	0.135
r_symmetry_hbond_refined	0.107
r_nbtor_other	0.085
r_chiral_restr	0.079
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3460
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	61

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction