3C3P | pdb_00003c3p

Crystal structure of a methyltransferase (NP_951602.1) from Geobacter sulfurreducens at 1.90 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.3	277	NANODROP, 0.2M Sodium chloride, 18.0% PEG 8000, 0.1M CAPS pH 10.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP	10.5	277	NANODROP, 0.2M Sodium chloride, 20.0% PEG 8000, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.88	α = 90
b = 76.044	β = 118.27
c = 85.173	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-11-20	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-10-25	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	1.00000	SSRL	BL11-1
2	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97939, 0.97953, 0.91840	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	28.318	99.9	0.056	0.056	7.8	3.8		69499			35.05

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.9	1.95	100		0.507	0.507	1.3	3.8	5126

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.9	28.318	69497	3515	99.87	0.201	0.199	0.2	0.232	0.23	RANDOM	29.203

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]
-0.41		0.24	-0.3		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.787
r_dihedral_angle_3_deg	11.803
r_dihedral_angle_4_deg	11.485
r_dihedral_angle_1_deg	2.457
r_scangle_it	1.918
r_angle_refined_deg	1.867
r_mcangle_it	1.805
r_angle_other_deg	1.496
r_scbond_it	1.273
r_mcbond_it	1.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.787
r_dihedral_angle_3_deg	11.803
r_dihedral_angle_4_deg	11.485
r_dihedral_angle_1_deg	2.457
r_scangle_it	1.918
r_angle_refined_deg	1.867
r_mcangle_it	1.805
r_angle_other_deg	1.496
r_scbond_it	1.273
r_mcbond_it	1.097
r_mcbond_other	0.252
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4466
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	161

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.