3HAZ | pdb_00003haz

Crystal structure of bifunctional proline utilization A (PutA) protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Partial model from MAD/SAD phasing from another crystal form

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	2M Ammonium sulfate, 0.1 M Tris-HCl pH 7.0. N-terminal His tag cleaved by TEV protease, which leaves Gly-His at N-terminus., VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.51	64.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.763	α = 90
b = 195.846	β = 121.48
c = 108.68	γ = 90

Symmetry
Space Group	C 1 2 1

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	NOIR-1		2007-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.000	ALS	4.2.2

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	2.1	43.27	100	0.103	0.103	5.386	3.8		172549

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)
	2.1	2.21	100		0.412	0.412	1.8	3.7	25188

Refinement

Statistics
Diffraction ID	Structure Solution 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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	combination of Se-Met MAD/SAD and MR	Partial model from MAD/SAD phasing from another crystal form	2.1	42.33	172521	8703	99.98	0.202	0.2	0.1954	0.233	0.2278	random	34.881

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]
-4.136		-0.515	-6.108		6.963

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.257
f_angle_d	0.86
f_chiral_restr	0.052
f_bond_d	0.005
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14647
Nucleic Acid Atoms
Solvent Atoms	795
Heterogen Atoms	295

Software

Software
Software Name	Purpose
SCALA	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	phasing
MOLREP	phasing