2Q1A | pdb_00002q1a

2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2-oxobutyrate

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q18

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	293	Na/K phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.83	α = 90
b = 128.83	β = 90
c = 224.4	γ = 90

Symmetry
Space Group	I 41 2 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	IMAGE PLATE	MAR scanner 345 mm plate	Osmic mirrors	2006-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.5	20	97	0.11	5.7	2.4	31603	31603

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	2.5	2.6	95.7		0.45	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	2Q18	2.5	19.66	30010	30010	1594	95.99	0.2354	0.23434	0.23	0.25565	0.25	RANDOM	44.579

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]
0.65			0.65		-1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.586
r_dihedral_angle_3_deg	14.178
r_dihedral_angle_4_deg	13.483
r_dihedral_angle_1_deg	5.736
r_scangle_it	1.364
r_angle_refined_deg	1.083
r_mcangle_it	0.933
r_scbond_it	0.8
r_mcbond_it	0.53
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.235
r_nbd_refined	0.188
r_xyhbond_nbd_refined	0.159
r_symmetry_vdw_refined	0.106
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2316
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
XDS	data reduction
XSCALE	data scaling
XFIT	data reduction