3ACZ | pdb_00003acz

Crystal structure of Entamoeba histolytica methionine gamma-lyase 1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	277	1.8M (NH4)2SO4, 0.1M cacodylate buffer, 0.1M Li3(C3H5O(COO)3), 0.1mM pyridozxal 5'-phosphate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.285	α = 90
b = 85.336	β = 101.96
c = 114.62	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	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.00000	Photon Factory	AR-NW12A

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	1.97	50	97.6	0.058	22.115	3.4		129357

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)
	1.97	2.04	97.1		0.388	3.5	3.4	12811

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.97	39.06	129283	6498	97.34	0.157	0.156	0.19	0.2111	RANDOM	26.92

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]
-0.15		0.08	-0.09		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.344
r_dihedral_angle_3_deg	15.272
r_dihedral_angle_4_deg	14.906
r_dihedral_angle_1_deg	5.507
r_scangle_it	3.482
r_scbond_it	2.205
r_angle_refined_deg	1.468
r_mcangle_it	1.21
r_mcbond_it	0.658
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11812
Nucleic Acid Atoms
Solvent Atoms	1005
Heterogen Atoms	72

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling