4A7Z | pdb_00004a7z

Complex of bifunctional aldos-2-ulose dehydratase with the reaction intermediate ascopyrone M

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A7K	PDB ENTRY 4A7K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		0.1 M BISTRIS-PROPANE, 0.2 M NACL, 16% PEG6000. CRYSTALS WERE OBTAINED BY CO-CRYSTALLISATION IN THE PRESENCE OF 0.2 M ANHYDROFRUCTOSE INCUBATED WITH 0,2M HYDROXYLAMINE, pH 7

Crystal Properties
Matthews coefficient	Solvent content
2.71	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.22	α = 90
b = 82.67	β = 90
c = 97.91	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	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.6	42	93.2	0.12	8.4	4		33047

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	2.6	2.7	99.3		0.54	2.2	3.6

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	PDB ENTRY 4A7K	2.6	41.33	31351	1674	97.94	0.19739	0.19376	0.19	0.26694	0.27	RANDOM	35.558

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]
-0.56			1.61		-1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.655
r_dihedral_angle_4_deg	20.189
r_dihedral_angle_3_deg	16.982
r_dihedral_angle_1_deg	7.193
r_angle_refined_deg	1.695
r_chiral_restr	0.107
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6801
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	24

Software

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