1VL8 | pdb_00001vl8

Crystal structure of Gluconate 5-dehydrogenase (TM0441) from Thermotoga maritima at 2.07 A resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G6K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	4.2	277	Acetate pH 4.2, 35% Glycerol, 0.4M NH4H2PO3 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.89	68.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.504	α = 90
b = 123.504	β = 90
c = 122.323	γ = 90

Symmetry
Space Group	P 43 21 2

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	APS	water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2004-02-20	M	SINGLE WAVELENGTH

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

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	1.96	50	89.42	0.088	16.01	6.89		61222			32.51

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	1.96	2.03	72.83		0.672	1.06	2.35	4917

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1g6k	2.07	43.67	50440	2715	91.5	0.15148	0.14999	0.16	0.17955	0.19	RANDOM	26.843

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]
-1.08			-1.08		2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.122
r_dihedral_angle_4_deg	14.893
r_dihedral_angle_3_deg	13.495
r_scangle_it	6.908
r_dihedral_angle_1_deg	5.97
r_scbond_it	5.163
r_mcangle_it	2.492
r_mcbond_it	2.181
r_angle_refined_deg	1.655
r_angle_other_deg	0.947
r_mcbond_other	0.521
r_nbd_refined	0.203
r_symmetry_vdw_other	0.197
r_nbd_other	0.176
r_nbtor_refined	0.175
r_symmetry_hbond_refined	0.159
r_symmetry_vdw_refined	0.146
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.097
r_nbtor_other	0.085
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3838
Nucleic Acid Atoms
Solvent Atoms	331
Heterogen Atoms	102

Software

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