4QQU

Crystal structure of the cobalamin-independent methionine synthase enzyme in a closed conformation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4L5Z	PDB ENTRY 4L5Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	298	50 mM sodium iodide, 27% w/v PEG3350, 0.25 mM BME, 0.15 mM zinc sulfate, 2 mM homocysteine, 5 mM 5-methyltetrahydrofolate triglutamate, 20 mM Tris-Cl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.978	α = 90
b = 99.102	β = 90
c = 103.902	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 315r		2014-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.97648	ALS	5.0.3

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	2.98	71.71	100	0.172	5.4	7.8	16415	16414

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	2.98	3.03	100		0.601

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4L5Z	2.98	71.71	16415	15543	828	99.93	0.18041	0.17544	0.2757	RANDOM	31.671

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]
-1.19			2.53		-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.45
r_dihedral_angle_3_deg	16.551
r_dihedral_angle_4_deg	14.594
r_dihedral_angle_1_deg	6.846
r_long_range_B_refined	4.234
r_long_range_B_other	4.234
r_mcangle_other	2.759
r_scangle_other	2.434
r_angle_refined_deg	1.635
r_scbond_other	1.426
r_mcangle_it	1.303
r_angle_other_deg	0.832
r_mcbond_it	0.762
r_mcbond_other	0.761
r_scbond_it	0.72
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5888
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	69

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling