2AAG | pdb_00002aag

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

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		c-alpha trace of density map resulting from a single-wavelength anomalous difference data set (using Hg's anomalous signal)

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.1838	0.23178	0.1844	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
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