1VR6

Crystal structure of Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase) (TM0343) from Thermotoga Maritima at 1.92 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	5.5	293	35.0% Ethylene-Glycol, 0.1M Acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.151	α = 90
b = 74.226	β = 90
c = 249.54	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 QUANTUM 315	fixed-height exit beam, toroidal focusing mirror	2004-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2		ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.92	47.76	98.79	0.065	23.07	3.57		102464			44.73

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	1.96	90.38		0.659	1.49	2.63	4594

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1RZM	1.92	47.76	97241	5111	98.54	0.1732	0.17089	0.21519	RANDOM	42.205

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]
0.01			-0.29		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.389
r_dihedral_angle_4_deg	20.19
r_dihedral_angle_3_deg	14.676
r_scangle_it	7.058
r_dihedral_angle_1_deg	5.943
r_scbond_it	5.247
r_mcangle_it	3.095
r_mcbond_it	2.113
r_angle_refined_deg	1.516
r_angle_other_deg	0.842
r_mcbond_other	0.604
r_symmetry_vdw_other	0.298
r_symmetry_vdw_refined	0.271
r_nbd_refined	0.213
r_nbd_other	0.192
r_xyhbond_nbd_refined	0.18
r_symmetry_hbond_refined	0.179
r_nbtor_refined	0.172
r_chiral_restr	0.093
r_nbtor_other	0.086
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10375
Nucleic Acid Atoms
Solvent Atoms	615
Heterogen Atoms

Software

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