1OK4 | pdb_00001ok4

Archaeal fructose 1,6-bisphosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5		9% (W/V) PEG 4000, 0.1 M NA ACETATE PH 5.0, 1-8% GLYCEROL, 100 MM DHAP

Crystal Properties
Matthews coefficient	Solvent content
2.3	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.4	α = 90
b = 157.3	β = 108.2
c = 101.5	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100				2002-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B		EMBL/DESY, HAMBURG	BW7B

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	40	90.2	0.071	13.6	3.6		125363

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	2.19	59.3		0.272	2.3	2.1

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 1OJX	2.1	36.51	125363	3203	100	0.164	0.163	0.2076	0.185	0.2275	RANDOM	10.04

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]
-0.07		0.07	-0.12		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.666
r_scangle_it	3.916
r_scbond_it	2.199
r_mcangle_it	1.295
r_angle_refined_deg	1.275
r_angle_other_deg	0.834
r_mcbond_it	0.603
r_symmetry_vdw_other	0.37
r_symmetry_vdw_refined	0.327
r_symmetry_hbond_refined	0.255
r_nbd_other	0.239
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.15
r_nbtor_other	0.086
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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_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	19358
Nucleic Acid Atoms
Solvent Atoms	641
Heterogen Atoms	90

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling