1VL1 | pdb_00001vl1

Crystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	0.2M (NH4)2HCitrate, 20% PEG-3350 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.93	35.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.733	α = 90
b = 75.146	β = 90
c = 148.443	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC		2004-04-02	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	1.55	50	79.46	0.075	16.59	3.86		24729			23.98

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	1.55	1.61	26.04		0.325	2.93	2.57	798

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	1PBT	1.55	37.11	23466	1262	79.32	0.16717	0.16523	0.18	0.20395	0.22	RANDOM	22.367

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]
-0.31			2.44		-2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.484
r_dihedral_angle_4_deg	16.694
r_dihedral_angle_3_deg	11.733
r_dihedral_angle_1_deg	6.249
r_scangle_it	3.979
r_scbond_it	2.733
r_angle_refined_deg	1.62
r_mcangle_it	1.535
r_mcbond_it	1.151
r_angle_other_deg	0.876
r_symmetry_vdw_other	0.364
r_mcbond_other	0.327
r_symmetry_vdw_refined	0.294
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.194
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.115
r_nbtor_other	0.083
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1766
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	13

Software

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