1W3T | pdb_00001w3t

Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDGal, D-Glyceraldehyde and pyruvate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W37	PDB ENTRY 1W37

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		0.1M HEPES PH6, 13% PEG4,000, 8% ISOPROPANOL, pH 6.00

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.43	α = 90
b = 131.733	β = 90
c = 132.859	γ = 90

Symmetry
Space Group	P 21 21 21

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 CCD		2004-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	39.8	99.9	0.08	7	7.8		85931		5	21.16

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	2.21	99.9		0.22	3.3	7.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1W37	2.1	40	77251	8678	99.9	0.155	0.15	0.15	0.204	0.2	RANDOM	21.08

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]
-0.719			0.914		-0.194

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.565
r_scangle_it	5.687
r_scbond_it	3.432
r_mcangle_it	1.949
r_angle_refined_deg	1.799
r_mcbond_it	1.1
r_nbtor_refined	0.317
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.17
r_symmetry_vdw_refined	0.152
r_chiral_restr	0.127
r_symmetry_hbond_refined	0.111
r_bond_refined_d	0.023
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9302
Nucleic Acid Atoms
Solvent Atoms	819
Heterogen Atoms	112

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing