1VLY

Crystal structure of a putative aminomethyltransferase (ygfz) from escherichia coli at 1.30 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	7.3	277	0.2M CaAcetate, 20.0% PEG-3350, No Buffer pH 7.3, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.814	α = 94.68
b = 50.08	β = 115.29
c = 52.014	γ = 116.46

Symmetry
Space Group	P 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 315	flat mirror	2004-07-05	M	SINGLE WAVELENGTH
2	1	x-ray		M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979508,0.885567	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.3	26.45	89.3	0.036	17.5	3.2		75749			19.89

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.3	1.37	61.5		0.339	3.2	2	7630

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.3	26.45	71946	3802	89.27	0.13572	0.13402	0.16785	RANDOM	14.06

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]
-0.24	0.37	-0.09	-0.14	0.28	0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.927
r_dihedral_angle_4_deg	12.108
r_dihedral_angle_3_deg	11.94
r_sphericity_free	6.506
r_dihedral_angle_1_deg	6.461
r_scangle_it	5.375
r_scbond_it	4.135
r_sphericity_bonded	3.452
r_mcangle_it	3.171
r_mcbond_it	2.427
r_rigid_bond_restr	1.938
r_angle_refined_deg	1.495
r_mcbond_other	1.411
r_angle_other_deg	1.052
r_symmetry_vdw_refined	0.378
r_symmetry_vdw_other	0.263
r_nbd_refined	0.224
r_symmetry_hbond_refined	0.201
r_nbd_other	0.192
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.15
r_metal_ion_refined	0.107
r_chiral_restr	0.089
r_nbtor_other	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2475
Nucleic Acid Atoms
Solvent Atoms	477
Heterogen Atoms	18

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
CCP4	data scaling