3GKB | pdb_00003gkb

Crystal structure of a putative enoyl-CoA hydratase from Streptomyces avermitilis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5	294	100mM Sodium acetate pH 5.0, 33% PEG 4000, 200mM Ammonium acetate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.461	α = 90
b = 87.502	β = 90
c = 154.447	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR CCD 165 mm		2009-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	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	1.8	77.224	99.9	0.107	0.107	12.5	7	74987	74217			13.7

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	1.8	1.9	100		0.259	0.259	5.6	7	10730

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.8	20	74184	74073	3727	99.85	0.172	0.171	0.18	0.206	0.22	RANDOM	20.445

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]
0.07			0.23		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.577
r_dihedral_angle_4_deg	19.492
r_dihedral_angle_3_deg	12.223
r_dihedral_angle_1_deg	5.038
r_scangle_it	4.07
r_scbond_it	2.535
r_mcangle_it	1.443
r_angle_refined_deg	1.399
r_angle_other_deg	0.959
r_mcbond_it	0.787

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.577
r_dihedral_angle_4_deg	19.492
r_dihedral_angle_3_deg	12.223
r_dihedral_angle_1_deg	5.038
r_scangle_it	4.07
r_scbond_it	2.535
r_mcangle_it	1.443
r_angle_refined_deg	1.399
r_angle_other_deg	0.959
r_mcbond_it	0.787
r_mcbond_other	0.226
r_chiral_restr	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6128
Nucleic Acid Atoms
Solvent Atoms	684
Heterogen Atoms	18

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

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.