7QON | pdb_00007qon

Monoclinic triose phosphate isomerase from Fasciola hepatica.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JK2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		291	0.2 M Li2SO4, 0.1 M ADA pH 6.5, 30 % v/v PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.393	α = 90
b = 110.464	β = 97.367
c = 118.143	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M-F		2015-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.51	51.809	99.1	0.059	0.999	10.9	3.2		167030

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.51	1.54			1.457	0.321

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2JK2	1.51	51.809	166994	8336	99.073	0.167	0.1651	0.18	0.1932	0.2	27.833

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]
-0.797		0.712	0.347		0.257

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.041
r_dihedral_angle_4_deg	20.23
r_dihedral_angle_3_deg	13.901
r_lrange_it	10.192
r_lrange_other	10.133
r_scangle_it	8.68
r_scangle_other	8.68
r_scbond_it	6.29
r_scbond_other	6.272
r_dihedral_angle_1_deg	6.269
r_mcangle_it	6.02
r_mcangle_other	6.014
r_mcbond_it	4.499
r_mcbond_other	4.491
r_angle_refined_deg	1.41
r_angle_other_deg	1.351
r_metal_ion_refined	0.272
r_nbd_other	0.271
r_symmetry_nbd_refined	0.231
r_nbd_refined	0.214
r_symmetry_nbd_other	0.178
r_xyhbond_nbd_refined	0.164
r_nbtor_refined	0.159
r_symmetry_xyhbond_nbd_other	0.149
r_symmetry_xyhbond_nbd_refined	0.137
r_ncsr_local_group_2	0.095
r_ncsr_local_group_6	0.091
r_ncsr_local_group_4	0.085
r_ncsr_local_group_5	0.084
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_1	0.079
r_chiral_restr	0.07
r_ncsr_local_group_3	0.069
r_bond_refined_d	0.008
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	7766
Nucleic Acid Atoms
Solvent Atoms	1090
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PARROT	phasing
MoRDa	phasing