6N94 | pdb_00006n94

Methylmalonyl-CoA decarboxylase in complex with 2-nitronate-propionyl-amino(dethia)-CoA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6N92

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	50 mM sodium chloride, 100 mM imidazole, 0.4 M Monosodium phosphate/1.6 M Dipotassium phosphate, 2% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.046	α = 90
b = 114.816	β = 90
c = 193.732	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	MARMOSAIC 300 mm CCD		2016-08-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.75	30	100	0.125	0.125	0.135	0.05	5.2	7.3	1422149	194971		-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	1.75	1.78	100		1.489	1.489	1.312	7.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6N92	1.75	29.29	175192	9164	94.03	0.1473	0.1457	0.16	0.1777	0.19	RANDOM	21.86

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]
-0.32			-0.15		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.653
r_dihedral_angle_4_deg	16.145
r_dihedral_angle_3_deg	14.169
r_dihedral_angle_1_deg	6.36
r_mcangle_it	2.719
r_angle_refined_deg	1.868
r_mcbond_other	1.851
r_mcbond_it	1.85
r_angle_other_deg	1.509
r_chiral_restr	0.116

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.653
r_dihedral_angle_4_deg	16.145
r_dihedral_angle_3_deg	14.169
r_dihedral_angle_1_deg	6.36
r_mcangle_it	2.719
r_angle_refined_deg	1.868
r_mcbond_other	1.851
r_mcbond_it	1.85
r_angle_other_deg	1.509
r_chiral_restr	0.116
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12246
Nucleic Acid Atoms
Solvent Atoms	1893
Heterogen Atoms	550

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.