1VP5

Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009) from Thermotoga maritima at 2.40 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	5.6	277	5.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.314	α = 90
b = 94.314	β = 90
c = 146.855	γ = 120

Symmetry
Space Group	P 65

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		2004-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

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	2.4	24.93	99.9	0.123	15.6	7.4		28944			49.56

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	2.4	2.46	100		0.83	2.4	7.4	2124

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	REFINEMENT STARTING MODEL	2.4	24.93	27471	1471	99.89	0.15363	0.15113	0.16	0.20258	0.21	RANDOM	39.279

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]
0.93	0.46		0.93		-1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.999
r_dihedral_angle_4_deg	19.905
r_dihedral_angle_3_deg	15.738
r_dihedral_angle_1_deg	9.909
r_scangle_it	6.228
r_scbond_it	4.762
r_mcangle_it	2.406
r_angle_refined_deg	1.672
r_mcbond_it	1.616
r_angle_other_deg	0.94
r_mcbond_other	0.486
r_symmetry_vdw_other	0.35
r_symmetry_vdw_refined	0.251
r_nbd_refined	0.2
r_nbd_other	0.192
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.089
r_nbtor_other	0.089
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4560
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	96

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling