2C0Z | pdb_00002c0z

The 1.6 A resolution crystal structure of NovW: a 4-keto-6-deoxy sugar epimerase from the novobiocin biosynthetic gene cluster of Streptomyces spheroides

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EP0	PDB ENTRY 1EP0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		25% SATURATED AMMONIUM SULFATE IN 100MM TRIS-HCL PH8.5, pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
2	36.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.354	α = 90
b = 59.354	β = 90
c = 109.03	γ = 90

Symmetry
Space Group	P 43 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		2002-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6		SRS	PX9.6

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	1.6	39	99.9	0.06	25.7	5.8		26449		3	15.5

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	1.6	1.64	99.9		0.36	3.9

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 1EP0	1.6	51.99	25098	1348	99.9	0.152	0.15	0.17	0.195	0.21	RANDOM	17.6

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]
0.38			0.38		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.122
r_scangle_it	4.379
r_scbond_it	2.774
r_mcangle_it	1.964
r_angle_other_deg	1.54
r_angle_refined_deg	1.492
r_mcbond_it	1.214
r_symmetry_vdw_other	0.348
r_nbd_other	0.258
r_nbd_refined	0.245
r_symmetry_hbond_refined	0.209
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.1
r_nbtor_other	0.091
r_bond_refined_d	0.014
r_gen_planes_other	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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_mcbond_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	1500
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling