8AYV | pdb_00008ayv

Crystal structure of the Malonyl-ACP Decarboxylase MadB from Pseudomonas putida

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	25% PEG 1500, 0.1 M SPG buffer at pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.739	α = 90
b = 58.282	β = 95.427
c = 57.131	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	PIXEL	DECTRIS EIGER2 XE 16M		2021-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.044	56.875	93.9	0.042	0.018	1	16	6.3		101763

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.044	1.107	53.8		0.755	0.46	0.626	1.3	3.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	AlphaFold	1.044	56.875	101763	5034	84.965	0.124	0.1223	0.12	0.1512	0.15	15.701

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]
0.153		-0.003	0.129		-0.276

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.626
r_dihedral_angle_4_deg	17.367
r_dihedral_angle_3_deg	11.242
r_rigid_bond_restr	7.94
r_dihedral_angle_1_deg	6.651
r_scbond_it	6.229
r_scbond_other	6.226
r_scangle_it	4.829
r_lrange_it	4.829
r_scangle_other	4.82
r_lrange_other	4.595
r_mcangle_it	2.663
r_mcangle_other	2.662
r_mcbond_it	2.592
r_mcbond_other	2.589
r_angle_refined_deg	2.008
r_angle_other_deg	1.619
r_xyhbond_nbd_refined	0.273
r_symmetry_xyhbond_nbd_refined	0.251
r_nbd_other	0.249
r_nbd_refined	0.23
r_symmetry_nbd_other	0.187
r_symmetry_nbd_refined	0.184
r_symmetry_xyhbond_nbd_other	0.182
r_nbtor_refined	0.179
r_ncsr_local_group_1	0.149
r_chiral_restr	0.128
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2376
Nucleic Acid Atoms
Solvent Atoms	391
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing