2IU4 | pdb_00002iu4

Dihydroxyacetone kinase operon co-activator Dha-DhaQ

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5		0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.5, 2 M AMMONIUM SULFATE

Crystal Properties
Matthews coefficient	Solvent content
3.54	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.897	α = 90
b = 99.897	β = 90
c = 188.566	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	1.96	40	99.9	0.1	11.17	5.39		77167		3

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	1.96	2.04	99.9		0.29	5.66	4.54

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.96	30	76689	1583	99.9	0.182	0.181	0.1813	0.209	0.2041	RANDOM	29.84

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]
0.67	0.33		0.67		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.142
r_dihedral_angle_4_deg	28.184
r_dihedral_angle_3_deg	16.03
r_dihedral_angle_1_deg	6.309
r_scangle_it	3.949
r_scbond_it	2.682
r_mcangle_it	1.752
r_angle_refined_deg	1.524
r_mcbond_it	1.363
r_symmetry_hbond_refined	0.395
r_nbtor_refined	0.329
r_nbd_refined	0.234
r_symmetry_vdw_refined	0.213
r_chiral_restr	0.201
r_xyhbond_nbd_refined	0.177
r_bond_refined_d	0.009
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_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	5125
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing