3LBF

Crystal structure of Protein L-isoaspartyl methyltransferase from Escherichia coli

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	288	Hepes-Na, monosodium dihydrogen phosphate, monopotassium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.3	α = 74
b = 55.06	β = 74.7
c = 67.49	γ = 85.57

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				2009-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.00

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	1.8	25	96.2	0.056	10.7	2.8		62259

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	1.8	1.9		95	0.207	3.9	2.8	8977

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2YXE	1.8	25	59103	3156	96.21	0.2151	0.2134	0.2472	RANDOM	42.2995

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]
0.49	0.02	-0.24	1.83	-2.91	-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.852
r_dihedral_angle_4_deg	19.166
r_dihedral_angle_3_deg	15.175
r_dihedral_angle_1_deg	5.474
r_scangle_it	3.512
r_scbond_it	2.165
r_mcangle_it	1.848
r_angle_refined_deg	1.24
r_mcbond_it	1.066
r_chiral_restr	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6117
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	140

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction