3IXL | pdb_00003ixl

Crystal structure of the Gly74Cys-Cys188Ser mutant of arylmalonate decarboxylase in the liganded form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DTV	PDB ENTRY 3DTV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	293	1.2M ammonium sulfate, 15%(w/v) PEG 5000, 10mM alpha-bromophenylacetate, 1%(v/v) dioxan, 70mM HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.392	α = 90
b = 63.353	β = 90
c = 82.413	γ = 90

Symmetry
Space Group	P 21 2 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 225 mm CCD	mirrors	2008-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0000	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.45	100	98.8	0.054				35026		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.45	1.48	70.8		0.246	5.14

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	PDB ENTRY 3DTV	1.45	20	33171	1756	95.89	0.17185	0.17072	0.17	0.19347	0.19	RANDOM	13.309

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]
-0.19			-0.3		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.461
r_dihedral_angle_4_deg	14.526
r_dihedral_angle_3_deg	11.843
r_dihedral_angle_1_deg	5.537
r_scangle_it	2.934
r_scbond_it	1.813
r_angle_refined_deg	1.298
r_mcangle_it	1.092
r_mcbond_it	0.668
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.461
r_dihedral_angle_4_deg	14.526
r_dihedral_angle_3_deg	11.843
r_dihedral_angle_1_deg	5.537
r_scangle_it	2.934
r_scbond_it	1.813
r_angle_refined_deg	1.298
r_mcangle_it	1.092
r_mcbond_it	0.668
r_nbtor_refined	0.305
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.154
r_symmetry_hbond_refined	0.104
r_chiral_restr	0.084
r_xyhbond_nbd_refined	0.084
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1703
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	21

Software

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

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.