3K7S | pdb_00003k7s

Complex of Trypanosoma cruzi ribose 5-phosphate isomerase type B with ribose 5-phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K7O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	20% (w/v) PEG 550 monomethyl ether, 0.1 M NaCl, 0.1 M Bicine, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.302	α = 90
b = 92.302	β = 90
c = 93.584	γ = 90

Symmetry
Space Group	P 21 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	ADSC QUANTUM 4		2009-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	93.659	99.3				63050

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	99.1		0.294	2.5

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	3K7O	1.9	40	63015	3203	99	0.172	0.17	0.17	0.196	0.2	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]
0.16			0.33		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.766
r_dihedral_angle_4_deg	17.452
r_dihedral_angle_3_deg	11.38
r_dihedral_angle_1_deg	4.75
r_scangle_it	2.343
r_scbond_it	1.398
r_angle_refined_deg	1.088
r_mcangle_it	0.841
r_mcbond_it	0.502
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.074
r_symmetry_hbond_refined	0.06
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4664
Nucleic Acid Atoms
Solvent Atoms	474
Heterogen Atoms	56

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing