3QDF | pdb_00003qdf

Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DFU	2dfu molecule A, protein only

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	MymaA.00471.a.A1 PW30262 at 26.1 mg/mL against PACT screen condition A12, 10 mM ZnCl2, 0.1 M NaOAc pH 5.0, 20% PEG 6000 and cryo-protected with 25% ethylene glycol, crystal tracking ID 218461a12, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.7	α = 90
b = 104.93	β = 90
c = 136.97	γ = 90

Symmetry
Space Group	I 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	RIGAKU SATURN 944+		2011-01-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.05	50	98.5	0.076	14.42	4.2	22070	21732		-3	31.963

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	2.05	2.1	91.9		0.461	2.9	2.8	1597

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 (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	2dfu molecule A, protein only	2.05	50	21644	1119	98.07	0.185	0.1826	0.2	0.2294	0.24	RANDOM	26.6039

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]
-0.02			1.14		-1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.929
r_dihedral_angle_4_deg	18.091
r_dihedral_angle_3_deg	13.046
r_dihedral_angle_1_deg	6.641
r_scangle_it	2.717
r_scbond_it	1.668
r_angle_refined_deg	1.377
r_mcangle_it	1.073
r_mcbond_it	0.62
r_chiral_restr	0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.929
r_dihedral_angle_4_deg	18.091
r_dihedral_angle_3_deg	13.046
r_dihedral_angle_1_deg	6.641
r_scangle_it	2.717
r_scbond_it	1.668
r_angle_refined_deg	1.377
r_mcangle_it	1.073
r_mcbond_it	0.62
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1862
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	14

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

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.