3BQB | pdb_00003bqb

Hexagonal kristal form of 2-keto-3-deoxyarabinonate dehydratase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q18	PDB ENTRY 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 Properties
Matthews coefficient	Solvent content
3.54	65.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.092	α = 90
b = 157.092	β = 90
c = 131.921	γ = 120

Symmetry
Space Group	P 61

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	2005-12-07	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	2.7	99.9	99.9	0.049	30.7	5.5	50804	50804			81.7

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	2.7	2.8	100		0.526	3.4	5.5	5043

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Q18	2.7	33.74	48004	48004	2562	99.1	0.24031	0.24031	0.23808	0.24	0.28355	0.28	RANDOM	63.124

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]
1.89	0.95		1.89		-2.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.128
r_dihedral_angle_3_deg	13.195
r_dihedral_angle_4_deg	12.988
r_dihedral_angle_1_deg	5.79
r_angle_refined_deg	0.996
r_angle_other_deg	0.709
r_scangle_it	0.708
r_mcangle_it	0.546
r_mcbond_it	0.515
r_scbond_it	0.451
r_nbd_refined	0.18
r_symmetry_vdw_other	0.173
r_nbtor_refined	0.165
r_nbd_other	0.162
r_symmetry_vdw_refined	0.128
r_xyhbond_nbd_refined	0.126
r_nbtor_other	0.075
r_chiral_restr	0.058
r_symmetry_hbond_refined	0.043
r_mcbond_other	0.035
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9024
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing