4UTU | pdb_00004utu

Structural and biochemical characterization of the N- acetylmannosamine-6-phosphate 2-epimerase from Clostridium perfringens

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.1 M PROPIONIC ACID, CACODYLATE, BIS-TRIS PROPANE BUFFER PH 8.0 AND 25% (W/V) PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.714	α = 90
b = 82.147	β = 92.48
c = 75.195	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 QUANTUM 315r			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	1.45	41.1	99.3	0.06	18	7		78204		4.3

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	1.45	1.53	95.8		0.46	4.3	5.9

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 4UTT	1.45	42	76612	1565	99.21	0.14062	0.14004	0.15	0.16915	0.18	RANDOM	18.602

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]
0.42		0.49	-0.07		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.755
r_dihedral_angle_4_deg	21.166
r_dihedral_angle_3_deg	12.77
r_dihedral_angle_1_deg	5.415
r_scangle_it	3.559
r_scbond_it	2.524
r_angle_refined_deg	1.607
r_mcangle_it	1.346
r_mcbond_it	1.134
r_angle_other_deg	0.981
r_mcbond_other	0.273
r_nbd_refined	0.226
r_symmetry_vdw_other	0.225
r_nbd_other	0.202
r_symmetry_hbond_refined	0.177
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.151
r_symmetry_vdw_refined	0.148
r_chiral_restr	0.097
r_nbtor_other	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
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	3502
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing