2PY6 | pdb_00002py6

Crystal structure of Methyltransferase FkbM (YP_546752.1) from Methylobacillus flagellatus KT at 2.20 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	NANODROP, 0.214M Ammonium nitrate, 14.0% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.66	α = 90
b = 119.17	β = 90
c = 122.58	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	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-04-29	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97926, 0.97891	SSRL	BL11-1

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	2.15	29.788	96.1	0.097	7.69	3.24		29426		-3	24.43

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	2.15	2.23	94.6		0.424	2.2

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 (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	MAD	THROUGHOUT	2.15	29.788	29425	1494	98.94	0.169	0.169	0.166	0.18	0.224	0.23	RANDOM	28.849

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]
0.07			0.63		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.33
r_dihedral_angle_4_deg	16.555
r_dihedral_angle_3_deg	11.007
r_scangle_it	6.114
r_scbond_it	4.971
r_dihedral_angle_1_deg	4.065
r_mcangle_it	2.946
r_mcbond_it	2.13
r_angle_refined_deg	1.747
r_angle_other_deg	1.065
r_mcbond_other	0.523
r_symmetry_vdw_other	0.265
r_xyhbond_nbd_refined	0.227
r_symmetry_hbond_refined	0.206
r_nbd_refined	0.194
r_nbtor_refined	0.179
r_nbd_other	0.174
r_symmetry_vdw_refined	0.15
r_chiral_restr	0.115
r_nbtor_other	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2956
Nucleic Acid Atoms
Solvent Atoms	379
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing