2DFU | pdb_00002dfu

Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Thermus Thermophilus HB8

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.4	295	sodium chloride, lithium sulfate, sodium citrate, pH 5.4, microbatch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.34	α = 90
b = 73.412	β = 111.78
c = 122.632	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	RIGAKU RAXIS V		2005-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.00	SPring-8	BL26B1

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	2.2	30	100	0.083	0.075	11.8	4.5	78745	78745			24.7

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	2.2	2.28	100		0.334	0.29	4.29	4.6	7869

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 1WZO	2.2	30	78392	78392	3956	99.8	0.198	0.197	0.197	0.2	0.224	0.2	RANDOM	41.2

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]
-1.36		4.45	5.54		-4.18

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.7
c_scangle_it	3.12
c_mcangle_it	2.13
c_scbond_it	2.07
c_angle_deg	1.4
c_mcbond_it	1.32
c_improper_angle_d	0.92
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7795
Nucleic Acid Atoms
Solvent Atoms	643
Heterogen Atoms

Software

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