3CVO | pdb_00003cvo

Crystal structure of a methyltransferase-like protein (spo2022) from silicibacter pomeroyi dss-3 at 1.80 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	277	NANODROP, 2.1M Ammonium sulfate, 1.5% PEG 400, 15.0% Glycerol, 0.1M HEPES pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.391	α = 90
b = 61.653	β = 97.45
c = 96.323	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 collimating mirror, toroid focusing mirror	2008-02-28	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162, 0.97914, 0.97932	SSRL	BL9-2

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	1.8	29.63	99.9	0.081	0.081	6.5	3.2		93599			21.483

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	1.8	1.85	99.8		0.648	0.648	1	3.2	6883

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	1.8	29.63	93597	4690	99.88	0.17	0.168	0.17	0.194	0.2	RANDOM	22.963

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]
-0.51		-1.37	1.14		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.344
r_dihedral_angle_4_deg	19.237
r_dihedral_angle_3_deg	13.878
r_scangle_it	7.224
r_dihedral_angle_1_deg	6.347
r_scbond_it	5.046
r_mcangle_it	2.936
r_mcbond_it	1.829
r_angle_refined_deg	1.592
r_angle_other_deg	1.375

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.344
r_dihedral_angle_4_deg	19.237
r_dihedral_angle_3_deg	13.878
r_scangle_it	7.224
r_dihedral_angle_1_deg	6.347
r_scbond_it	5.046
r_mcangle_it	2.936
r_mcbond_it	1.829
r_angle_refined_deg	1.592
r_angle_other_deg	1.375
r_mcbond_other	0.684
r_chiral_restr	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6003
Nucleic Acid Atoms
Solvent Atoms	496
Heterogen Atoms	213

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.