4K7G | pdb_00004k7g

Crystal structure of a 3-hydroxyproline dehydratse from agrobacterium vitis, target efi-506470, with bound pyrrole 2-carboxylate, ordered active site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TM0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffusion	4.6	298	Protein (10 mM Tris, 20 mM pyrrole 2-carboxylate, TEV Treated, Cleavage Unverified); Reservoir (0.1 M Sodium Acetate Trihydrate, 1 M di-Ammonium Hydrogen citrate (MCSG4 C6)); Cryoprotection (Reservoir+20% glycerol), pH 4.6, sitting drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.04	69.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.584	α = 90
b = 122.584	β = 90
c = 167.593	γ = 90

Symmetry
Space Group	P 43 21 2

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	RAYONIX 225 HE	MIRRORS	2012-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-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	33.52	100	0.17	0.17	11.6	3.8	86628	86628			19.8

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	2.11	100		0.836	0.836	3.3	13.2	12481

Refinement

Statistics
Diffraction ID	Structure Solution 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	1TM0	2	32.981	86532	86532	4336	99.99	0.1379	0.1379	0.1364	0.14	0.166	0.17	RANDOM	27.0431

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.789
f_angle_d	1.311
f_chiral_restr	0.076
f_bond_d	0.011
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5148
Nucleic Acid Atoms
Solvent Atoms	780
Heterogen Atoms	46

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.