2HK8 | pdb_00002hk8

Crystal structure of shikimate dehydrogenase from aquifex aeolicus at 2.35 angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HK7	PDB ENTRY 2HK7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	292	12% PEG20K, 0.1M MES (pH 6.4-6.6), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.361	α = 94.64
b = 73.96	β = 94.16
c = 192.107	γ = 91.81

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 4		2000-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B	1.05517	NSLS	X9B

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	2.35	30	87.2	0.053	12.1	2	74160	74160			34.6

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)
	2.35	2.43	44.8		0.275	2.4	1.7

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 (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 2HK7	2.35	28.4	71656	71656	3638	84.2	0.214	0.214	0.21	0.265	0.26	RANDOM	33.4

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]
4.03	-0.75	-1.42	0.11	-4.25	-4.15

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.5
c_scangle_it	4.39
c_scbond_it	3.08
c_mcangle_it	2.96
c_mcbond_it	1.91
c_angle_deg	1.3
c_improper_angle_d	0.96
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16797
Nucleic Acid Atoms
Solvent Atoms	626
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
PHASER	phasing