5IBX | pdb_00005ibx

1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM) from Streptococcus pneumoniae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M9Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	Protein: 7.5mg/ml, 0.25M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 5mM BME; Screen: Classics II(F12), 0.2M Sodium chloride, 0.1M HEPES (pH 7.5), 25%(w/v) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.16	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.845	α = 75.43
b = 84.351	β = 65.97
c = 92.463	γ = 62.03

Symmetry
Space Group	P 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	MARMOSAIC 300 mm CCD	C(111)	2014-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.65	30	97.1	0.083	0.083	0.757	14.8	3.9		225519		-3	20.1

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	1.65	1.68	95.5		0.622	2.3	3.9

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	3M9Y	1.65	29.69	212575	11243	97.08	0.19796	0.19617	0.2	0.23154	0.24	RANDOM	22.805

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]
-1.41	0.22	-0.08	0.05	-0.12	1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.575
r_dihedral_angle_4_deg	10.791
r_dihedral_angle_3_deg	10.239
r_long_range_B_refined	5.727
r_long_range_B_other	5.393
r_dihedral_angle_1_deg	3.513
r_scangle_other	1.72
r_angle_refined_deg	1.458
r_mcangle_it	1.259
r_mcangle_other	1.259
r_scbond_it	1.106
r_scbond_other	1.106
r_angle_other_deg	0.86
r_mcbond_it	0.806
r_mcbond_other	0.805
r_chiral_restr	0.085
r_gen_planes_refined	0.013
r_bond_refined_d	0.011
r_gen_planes_other	0.01
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14787
Nucleic Acid Atoms
Solvent Atoms	2372
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing