4OMA | pdb_00004oma

The crystal structure of methionine gamma-lyase from Citrobacter freundii in complex with L-cycloserine pyridoxal-5'-phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RFV	PDB ENTRY 2RFV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	303	5% PEG2000 MME, 50 mM Tris-HCl, 0.2 mM PLP, 0.25% DTT, pH 8.5, soaked in 50 mM L-cycloserine for 7 minutes, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.27	α = 90
b = 122.89	β = 90
c = 126.61	γ = 90

Symmetry
Space Group	I 2 2 2

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	MAR scanner 345 mm plate		2005-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.843	EMBL/DESY, HAMBURG	BW7B

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	1.6	15	94.5	0.048	17.28	4.5	55080	55080			26.8

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	1.6	1.65	94.3		0.396	3.6	3.9	4606

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	PDB ENTRY 2RFV	1.6	15	53896	53896	2893	97.48	0.142	0.142	0.139	0.14	0.197	0.2	RANDOM	28.688

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]
5.51			-2.81		-2.7

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	48.856
r_dihedral_angle_2_deg	37.696
r_sphericity_bonded	22.149
r_dihedral_angle_4_deg	18.427
r_dihedral_angle_3_deg	12.979
r_long_range_B_refined	7.555
r_scangle_other	7.364
r_rigid_bond_restr	7.26
r_long_range_B_other	7.248
r_scbond_it	6.376
r_scbond_other	6.374
r_dihedral_angle_1_deg	6.35
r_mcangle_it	5.993
r_mcangle_other	5.96
r_mcbond_it	4.757
r_mcbond_other	4.738
r_angle_refined_deg	1.943
r_angle_other_deg	1.014
r_chiral_restr	0.144
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2993
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	57

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASES	phasing
REFMAC	refinement
PROCESS	data reduction
PROCESS	data scaling