1TJ1 | pdb_00001tj1

Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with L-lactate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K87	PDB ENTRY 1k87

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7	295	13-15% PEG 3000, 60-190mM citrate buffer, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.9	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.814	α = 90
b = 141.124	β = 90
c = 146.015	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	CUSTOM-MADE	APS 19ID	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)	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	2	99	98	0.076	0.076	23	5.9	51161	50059			40

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	2	2.07	91		0.469	0.469	2.1	4.4	4618

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1k87	2	40.49	50055	47562	2493	98	0.216	0.2161	0.2141	0.22	0.25522	0.26	RANDOM	29.148

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]
0.45			3.66		-4.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.533
r_scangle_it	3.466
r_scbond_it	2.174
r_angle_refined_deg	1.403
r_mcangle_it	1.372
r_angle_other_deg	0.838
r_mcbond_it	0.732
r_symmetry_vdw_other	0.287
r_nbd_other	0.236
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.105
r_nbtor_other	0.084
r_chiral_restr	0.08
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	3474
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	59

Software

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