3GGO

Crystal structure of prephenate dehydrogenase from A. aeolicus with HPP and NADH

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G5C	pdb entry 2G5C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	100mM HEPES, 48% MPD, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.496	α = 90
b = 92.481	β = 90
c = 164.083	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	SBC-2		2007-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

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	2.15	46.24	96.4	0.048	47.3	9.1		66487		1.3

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	2.15	2.19	67.5		0.52	1.3	4.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2G5C	2.15	46.22	66783	64377	2030	96.29	0.2189	0.21755	0.262	RANDOM	38.906

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]
0.62			-0.18		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.644
r_dihedral_angle_4_deg	19.858
r_dihedral_angle_3_deg	19.114
r_dihedral_angle_1_deg	6.494
r_scangle_it	3.936
r_scbond_it	2.67
r_angle_refined_deg	1.804
r_mcangle_it	1.502
r_mcbond_it	0.883
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.234
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.155
r_symmetry_vdw_refined	0.15
r_chiral_restr	0.126
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8922
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	202

Software

Software
Software Name	Purpose
HKL-3000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling