1VKE

Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response (TM1620) from Thermotoga maritima at 1.56 A resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P8C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	5.5 MES 25 MPD 0.2 Li2SO4, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.69	53.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.922	α = 90
b = 67.975	β = 97.52
c = 90.077	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	CCD	ADSC		2003-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.56	50	92.29	0.04	32.69	3.8		106734			30.49

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.56	1.62	55.27		0.48	1.32	1.78	6403

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1P8C	1.56	44.65	101346	5361	92.21	0.15918	0.15816	0.17834	RANDOM	15.887

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]
-0.77		-0.85	-0.82		1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.844
r_dihedral_angle_4_deg	23.032
r_dihedral_angle_3_deg	11.943
r_scangle_it	7.281
r_scbond_it	4.77
r_dihedral_angle_1_deg	4.622
r_mcangle_it	2.732
r_mcbond_it	1.956
r_angle_refined_deg	1.44
r_angle_other_deg	0.863
r_mcbond_other	0.48
r_nbd_refined	0.322
r_symmetry_vdw_other	0.269
r_nbd_other	0.171
r_xyhbond_nbd_refined	0.171
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.095
r_nbtor_other	0.082
r_symmetry_vdw_refined	0.078
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	4870
Nucleic Acid Atoms
Solvent Atoms	435
Heterogen Atoms	68

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement