3N73 | pdb_00003n73

Crystal structure of a putative 4-hydroxy-2-oxoglutarate aldolase from Bacillus cereus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	295	0.1M BIS-TRIS PH6.5, 0.2M NACL, 25% PEG3350, VAPOR DIFFUSION - HANGING DROP, TEMPERATURE 273K, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.066	α = 90
b = 166.644	β = 90
c = 37.279	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 QUANTUM 315	MIRROR	2008-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9793	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.05	50	99.3	0.108	0.108	26.371	7.7	30820	30820		-3	31.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.05	2.09	66.6		0.673	0.673	3.3	7.2	1452

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	2.07	50	29151	29151	1561	96.86	0.17161	0.17161	0.16892	0.18	0.22128	0.19	RANDOM	32.068

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]
-0.66			0.48		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.718
r_dihedral_angle_4_deg	19.409
r_dihedral_angle_3_deg	12.692
r_dihedral_angle_1_deg	6.145
r_scangle_it	3.479
r_scbond_it	2.093
r_angle_refined_deg	1.441
r_mcangle_it	1.159
r_angle_other_deg	0.932
r_mcbond_it	0.659
r_mcbond_other	0.196
r_chiral_restr	0.084
r_bond_refined_d	0.016
r_bond_other_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3775
Nucleic Acid Atoms
Solvent Atoms	327
Heterogen Atoms	3

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing