6N95

Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EF8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	200 mM sodium chloride, 100 mM imidazole, 0.4 Monosodium phosphate/1.6 M Dipotassium phosphate, 4% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.927	α = 90
b = 114.421	β = 90
c = 193.43	γ = 90

Symmetry
Space Group	P 21 21 21

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 MX300HE		2017-02-08	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)	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	1.798	30	100	0.165	0.165	0.177	0.065	4.9	7.3		178862		-3

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	1.8	1.86	100		1.395	1.395	1.4	7.2

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-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1EF8	1.798	19.997	178638	8931	99.688	0.1593	0.1922	25.421

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]
-0.009			0.008		0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.232
r_dihedral_angle_4_deg	16.825
r_dihedral_angle_3_deg	14.005
r_lrange_it	6.264
r_lrange_other	6.256
r_dihedral_angle_1_deg	6.23
r_scangle_it	5.097
r_scangle_other	5.096
r_scbond_it	3.381
r_scbond_other	3.381
r_mcangle_it	2.773
r_mcangle_other	2.773
r_mcbond_it	1.993
r_mcbond_other	1.993
r_angle_refined_deg	1.724
r_angle_other_deg	1.042
r_metal_ion_refined	0.33
r_symmetry_nbd_refined	0.33
r_nbd_other	0.266
r_nbd_refined	0.223
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.138
r_symmetry_xyhbond_nbd_refined	0.125
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_other	0.024
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_symmetry_metal_ion_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12246
Nucleic Acid Atoms
Solvent Atoms	1777
Heterogen Atoms	713

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing