2Q1C | pdb_00002q1c

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q18

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 = 129.29	α = 90
b = 129.29	β = 90
c = 223.09	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	2.8	19.5	97.1	0.123	8.1	3.4	22992	22992

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	2.8	2.9	99.3		0.446	3

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	1Q18	2.8	19.48	21834	21834	1156	97.47	0.24084	0.23953	0.24	0.26565	0.26	RANDOM	43.833

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]
1.79			1.79		-3.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.184
r_dihedral_angle_4_deg	15.149
r_dihedral_angle_3_deg	12.862
r_dihedral_angle_1_deg	5.271
r_angle_refined_deg	1.028
r_scangle_it	0.672
r_mcangle_it	0.648
r_scbond_it	0.384
r_mcbond_it	0.361
r_nbtor_refined	0.299
r_symmetry_hbond_refined	0.193
r_xyhbond_nbd_refined	0.176
r_nbd_refined	0.166
r_symmetry_vdw_refined	0.113
r_metal_ion_refined	0.099
r_chiral_restr	0.085
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
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_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	88
Heterogen Atoms	8

Software

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