2AAG

Crystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	35% (v/v) 1,6-hexanediol, 200 mM MgCl2, and 100 mM Tris-Cl buffer, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.709	α = 90
b = 82.105	β = 101.15
c = 77.603	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	IMAGE PLATE	RIGAKU RAXIS IV	Osmic Blue Max-Flux Confocal optical system	2004-01-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.83	30	96.4	0.072	12.2	8.4	63310	60986		2	22.45

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	c-alpha trace of density map resulting from a single-wavelength anomalous difference data set (using Hg's anomalous signal)	1.85	19.21	60612	55695	2992	96.82	0.1783	0.181	0.17826	0.23178	RANDOM	23.573

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]
-0.48		-1.58	0.09		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.146
r_sphericity_free	5.252
r_scangle_it	4.225
r_scbond_it	2.628
r_angle_refined_deg	2.325
r_rigid_bond_restr	1.797
r_mcangle_it	1.719
r_sphericity_bonded	1.104
r_mcbond_it	1.016
r_symmetry_hbond_refined	0.366

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.146
r_sphericity_free	5.252
r_scangle_it	4.225
r_scbond_it	2.628
r_angle_refined_deg	2.325
r_rigid_bond_restr	1.797
r_mcangle_it	1.719
r_sphericity_bonded	1.104
r_mcbond_it	1.016
r_symmetry_hbond_refined	0.366
r_symmetry_vdw_refined	0.346
r_xyhbond_nbd_refined	0.233
r_nbd_refined	0.222
r_chiral_restr	0.18
r_bond_refined_d	0.028
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5952
Nucleic Acid Atoms
Solvent Atoms	807
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.