3IXM | pdb_00003ixm

Structure of the Gly74Cys mutant of arylmalonate decarboxylase in the sulfate ion associated form

X-RAY DIFFRACTION

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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	6.2	293	1.2M ammonium sulfate, 15%(w/v) glycerol, 0.1M HEPES, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.73	α = 90
b = 100.73	β = 90
c = 54.165	γ = 120

Symmetry
Space Group	H 3

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	mirror	2008-04-22	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	1.9	100	94.2	0.053				16054	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)
	1.9	1.93	100		0.129

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3DTV	1.9	20	15236	804	99.78	0.18311	0.18002	0.24462	0.262	RANDOM	23.296

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]
-0.5	-0.25		-0.5		0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.095
r_dihedral_angle_4_deg	20.903
r_dihedral_angle_3_deg	16.501
r_dihedral_angle_1_deg	6.347
r_scangle_it	4.739
r_scbond_it	2.958
r_mcangle_it	1.824
r_angle_refined_deg	1.718
r_mcbond_it	1.097
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.289
r_symmetry_vdw_refined	0.239
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.2
r_chiral_restr	0.121
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1673
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	10

Software

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