3E8X | pdb_00003e8x

Putative NAD-dependent epimerase/dehydratase from Bacillus halodurans.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	294	40% PEG-300, 0.1 M phosphate-citrate buffer, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.687	α = 90
b = 113.687	β = 90
c = 63.645	γ = 90

Symmetry
Space Group	P 41 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 QUANTUM 315		2008-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-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	2.1	50	95.7	0.089	51.6	15	24007	24007			50.6

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	2.1	2.14	73.7		0.848	2.42	11.3	914

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.1	50	23940	23940	1225	95.39	0.173	0.173	0.172	0.1721	0.193	0.1914	RANDOM	49.399

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]
-1.87			-1.87		3.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.226
r_dihedral_angle_4_deg	17.189
r_dihedral_angle_3_deg	14.907
r_dihedral_angle_1_deg	6.278
r_scangle_it	2.643
r_scbond_it	2.027
r_angle_refined_deg	1.705
r_angle_other_deg	1.058
r_mcangle_it	0.995
r_mcbond_it	0.767
r_symmetry_vdw_other	0.272
r_mcbond_other	0.22
r_symmetry_hbond_refined	0.217
r_nbd_refined	0.21
r_nbd_other	0.209
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.17
r_symmetry_vdw_refined	0.127
r_chiral_restr	0.098
r_nbtor_other	0.087
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1643
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	49

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing