6BOO

Crystal structure of 2-methylcitrate synthase from Aspergillus fumigatus with oxaloacetate and coenzyme-A.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UQO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1 M Bis-Tris pH 6.5 28% PEGMME2000 1.0 mM oxaloacetate 1.0 mM coenzyme-A

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.882	α = 90
b = 68.785	β = 89.93
c = 123.997	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	CCD	RAYONIX MX300-HS		2016-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	50	94.6	0.068	0.068	0.103	0.056	14.1	2.9		47339		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64	95.4		0.437	0.437	0.622	0.346	2.12	2.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5UQO	2.6	40	43765	2163	94.58	0.20091	0.19913	0.23683	RANDOM	42.361

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]
2.21		-0.55	0.7		-2.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.309
r_dihedral_angle_4_deg	19.757
r_dihedral_angle_3_deg	14.946
r_dihedral_angle_1_deg	5.311
r_angle_other_deg	3.627
r_long_range_B_refined	3.59
r_long_range_B_other	3.59
r_mcangle_it	2.231
r_mcangle_other	2.231
r_scangle_other	1.828
r_angle_refined_deg	1.514
r_mcbond_it	1.239
r_mcbond_other	1.239
r_scbond_it	1.002
r_scbond_other	1.002
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_other	0.011
r_gen_planes_refined	0.008
r_bond_other_d
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	13518
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms	141

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
HKL-3000	phasing