3JYO

Quinate dehydrogenase from Corynebacterium glutamicum in complex with NAD

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	293	1.6 M tri-sodium citrate, 0 up to 62.5 mM cobalt chloride, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.45	α = 90
b = 63.28	β = 94.46
c = 36.34	γ = 90

Symmetry
Space Group	C 1 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	100	IMAGE PLATE	MAR scanner 345 mm plate		2007-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.8423	EMBL/DESY, HAMBURG	BW7B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	10	93.1	0.065	0.065	34	3.8	147745	137551			17.18

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.04	85.9		0.615	0.615	2.05	3.1	14795

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2nlo	1	10	147745	137551	6770	93.1	0.16482	0.16482	0.16326	0.19421	Random	17.18

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.564
r_dihedral_angle_4_deg	16.513
r_dihedral_angle_3_deg	11.673
r_sphericity_free	9.91
r_sphericity_bonded	8.612
r_mcbond_other	6.118
r_dihedral_angle_1_deg	5.928
r_scangle_it	4.689
r_scbond_it	3.836
r_angle_other_deg	3.393
r_rigid_bond_restr	3.075
r_mcangle_it	3.056
r_mcbond_it	2.759
r_angle_refined_deg	1.764
r_symmetry_vdw_other	0.353
r_nbd_refined	0.254
r_nbd_other	0.23
r_symmetry_vdw_refined	0.188
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.166
r_symmetry_hbond_refined	0.158
r_chiral_restr	0.106
r_nbtor_other	0.09
r_bond_refined_d	0.017
r_bond_other_d	0.013
r_gen_planes_other	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2075
Nucleic Acid Atoms
Solvent Atoms	441
Heterogen Atoms	44

Software

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