2OX4

Crystal structure of putative dehydratase from Zymomonas mobilis ZM4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GL5	PDB entry 2GL5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	100mM Tris-HCl, pH 8.5, 30% PEG 4000, 200mM Lithium sulfate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 190.178	α = 90
b = 190.409	β = 90
c = 85.922	γ = 90

Symmetry
Space Group	P 21 21 2

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	MIRRORS	2006-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97960	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	50	100	0.094	0.075	4.8	6.7	288410	288410		-5	16.777

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	1.86	99.8		0.48	0.43	2.2	6.2	28540

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2GL5	1.8	20	278981	278981	8758	99.64	0.14513	0.14513	0.14386	0.18553	RANDOM	18.369

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]
-0.18			0.23		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.12
r_dihedral_angle_4_deg	18.864
r_dihedral_angle_3_deg	15.781
r_scangle_it	8.56
r_dihedral_angle_1_deg	7.896
r_scbond_it	6.099
r_mcangle_it	4.108
r_mcbond_it	3.18
r_angle_refined_deg	1.171
r_nbtor_refined	0.309
r_nbd_refined	0.181
r_xyhbond_nbd_refined	0.174
r_symmetry_hbond_refined	0.169
r_chiral_restr	0.157
r_symmetry_vdw_refined	0.155
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24692
Nucleic Acid Atoms
Solvent Atoms	3160
Heterogen Atoms	96

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling