4ODI | pdb_00004odi

2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 from Toxoplasma gondii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XQ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein - 7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3, Screen - Classics II (G12), 0.2M Magnesium chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.182	α = 90
b = 149.474	β = 90
c = 72.12	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	MARMOSAIC 225 mm CCD	Beryllium lenses	2013-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.6	30	100	0.106	0.106	18.3	7.3	33033	33033		-3	52

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64	100		0.645	0.645	3.3	7.4	1604

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1XQ9	2.6	29.72	31317	31317	1671	99.77	0.19925	0.19925	0.19717	0.2	0.23881	0.24	RANDOM	56.296

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]
-1.48			2.24		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.112
r_dihedral_angle_3_deg	11.868
r_dihedral_angle_4_deg	11.554
r_long_range_B_refined	6.815
r_long_range_B_other	6.815
r_scangle_other	4.75
r_mcangle_other	3.542
r_mcangle_it	3.541
r_scbond_it	3.003
r_scbond_other	3.003
r_dihedral_angle_1_deg	2.382
r_mcbond_it	2.268
r_mcbond_other	2.255
r_angle_refined_deg	1.626
r_angle_other_deg	1.217
r_chiral_restr	0.092
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7719
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	4

Software

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