2IFX | pdb_00002ifx

Crystal structure of a putative 4-methylmuconolactone methylisomerase (YP_295714.1) from Ralstonia eutropha JMP134 at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	6	277	0.2M Ca(OAc)2, 20.0% PEG-8000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.06	α = 90
b = 46.06	β = 90
c = 124.16	γ = 90

Symmetry
Space Group	P 43

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	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-08-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.94926, 0.97925, 0.97939	APS	23-ID-D

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	25.743	94.7	0.045	10.34			17384			44.084

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	2.07	80		0.328	2.5		2702

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2	25.743	17337	882	99.29	0.173	0.171	0.18	0.202	0.21	RANDOM	48.388

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]
-0.09			-0.09		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.788
r_dihedral_angle_4_deg	14.942
r_dihedral_angle_3_deg	11.174
r_scangle_it	6.071
r_scbond_it	4.729
r_dihedral_angle_1_deg	3.378
r_mcangle_it	2.592
r_mcbond_it	2.037
r_angle_refined_deg	1.493
r_angle_other_deg	0.861
r_mcbond_other	0.409
r_symmetry_vdw_other	0.285
r_nbd_refined	0.209
r_nbd_other	0.198
r_symmetry_vdw_refined	0.193
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.147
r_nbtor_other	0.088
r_chiral_restr	0.073
r_bond_refined_d	0.012
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	1638
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	13

Software

Software
Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing
RESOLVE	phasing