4NU7 | pdb_00004nu7

2.05 Angstrom Crystal Structure of Ribulose-phosphate 3-epimerase 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	3QC3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	295	Protein: 7.4 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (A1), 2M Ammonium sulfate, 0.1M Citric acid pH 3.5. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.51	α = 90
b = 138.51	β = 90
c = 349.329	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MARMOSAIC 225 mm CCD	Beryllium lenses	2012-11-18	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	2.05	30	100	0.072	0.072	20.1	4.5	81012	81012		-3	32.6

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	2.05	2.09	100		0.615	0.615	2.4	4.5	3999

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	3QC3	2.05	29.88	76865	76865	4056	99.88	0.15126	0.15126	0.14941	0.16	0.18685	0.19	RANDOM	39.93

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]
0.12	0.06		0.12		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.956
r_dihedral_angle_4_deg	19.199
r_dihedral_angle_3_deg	11.142
r_long_range_B_refined	7.956
r_long_range_B_other	7.737
r_scangle_other	4.703
r_scbond_it	3.164
r_dihedral_angle_1_deg	3.112
r_scbond_other	2.997
r_mcangle_other	2.732
r_mcangle_it	2.73
r_mcbond_it	1.834
r_mcbond_other	1.833
r_angle_refined_deg	1.434
r_angle_other_deg	0.719
r_chiral_restr	0.087
r_gen_planes_refined	0.019
r_gen_planes_other	0.017
r_bond_refined_d	0.01
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6761
Nucleic Acid Atoms
Solvent Atoms	513
Heterogen Atoms	69

Software

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