6VYE | pdb_00006vye

6-phosphogluconolactonase from Trypanosoma cruzi

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EB9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.3	298	0.1 M sodium citrate, 3.5 mM DTT, cryo-soak in 30% glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.77	α = 90
b = 63.39	β = 94.91
c = 79.32	γ = 90

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 210		2005-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9796	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.95	50.9	95.8	0.245	0.288	0.15	0.971	4.9	3.6		49639

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	77.7		1.669	2.014	1.106	0.472		3.1

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 (All)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3eb9	1.95	49.497	49552	2543	95.329	0.233	0.2312	0.2699	24.828

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]
1.496		-0.389	-2.648		1.201

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.677
r_dihedral_angle_3_deg	16.495
r_dihedral_angle_4_deg	10.893
r_dihedral_angle_1_deg	7.337
r_lrange_it	6.49
r_lrange_other	6.49
r_scangle_it	4.221
r_scangle_other	4.22
r_mcangle_it	3.509
r_mcangle_other	3.508
r_scbond_it	2.688
r_scbond_other	2.688
r_mcbond_it	2.185
r_mcbond_other	2.184
r_angle_refined_deg	1.626
r_angle_other_deg	1.287
r_nbd_other	0.215
r_nbd_refined	0.213
r_symmetry_xyhbond_nbd_refined	0.203
r_xyhbond_nbd_refined	0.197
r_symmetry_nbd_refined	0.186
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.151
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.075
r_xyhbond_nbd_other	0.073
r_ncsr_local_group_1	0.066
r_symmetry_xyhbond_nbd_other	0.016
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4059
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	33

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing