3CQK | pdb_00003cqk

Crystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE (form B) complex with Zn2+ and sulfate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CQH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	294	PEG 8000, Li2SO4, pH 8.5, vapor diffusion, hanging drop, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.028	α = 90
b = 132.55	β = 90
c = 82.079	γ = 90

Symmetry
Space Group	C 2 2 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			2007-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9798	APS	31-ID

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	2.32	50	92.4	0.078	10.7	7		43820			36.4

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	2.32	2.4	65.5		0.344		3.6	3131

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	3CQH	2.33	44.24	23386	1151	93.65	0.188	0.187	0.1811	0.211	0.2038	RANDOM	33.191

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]
1.6			-1.05		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.634
r_dihedral_angle_4_deg	17.98
r_dihedral_angle_3_deg	15.75
r_dihedral_angle_1_deg	6.405
r_scangle_it	2.893
r_scbond_it	1.817
r_angle_refined_deg	1.326
r_mcangle_it	1.28
r_mcbond_it	0.759
r_symmetry_vdw_refined	0.311
r_nbtor_refined	0.298
r_symmetry_hbond_refined	0.205
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.094
r_metal_ion_refined	0.026
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4384
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	14

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling