5TJR | pdb_00005tjr

X-ray Crystal structure of a methylmalonate semialdehyde dehydrogenase from Pseudomonas sp. AAC

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZZ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	281	Protein at 5 mg/mL with added acetyl-CoA; crystal conditions were 100 mM bis-tris propane at pH 7.6, 24% PEG 3350, 210 mM trisodium citr ate in 150 plus 150 nL drops.

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.891	α = 90
b = 156.631	β = 90
c = 192.246	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	ADSC QUANTUM 315		2015-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.95	49.6	99.9	0.178	0.998	11.5	14.7		74332

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3.01	100		1.607	0.818	2	15

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	4zz7	2.95	49	70516	3714	99.86	0.21417	0.21236	0.22	0.24862	0.25	RANDOM	72.029

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]
-4.13			7.93		-3.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.035
r_dihedral_angle_4_deg	19.73
r_dihedral_angle_3_deg	17.191
r_long_range_B_refined	14.274
r_long_range_B_other	14.274
r_scangle_other	8.656
r_mcangle_other	8.043
r_mcangle_it	8.042
r_dihedral_angle_1_deg	5.984
r_scbond_it	5.306
r_scbond_other	5.306
r_mcbond_it	5.171
r_mcbond_other	5.166
r_angle_refined_deg	1.686
r_angle_other_deg	1.058
r_chiral_restr	0.106
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	20813
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	135

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing