2QNE | pdb_00002qne

Crystal structure of putative methyltransferase (ZP_00558420.1) from Desulfitobacterium hafniense Y51 at 2.30 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	NANODROP, 1.4M Na3Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP	7.5	277	NANODROP, 1.4M Na3Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.863	α = 90
b = 123.863	β = 90
c = 122.844	γ = 120

Symmetry
Space Group	P 32 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)	2007-02-09	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-02-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.99184	SSRL	BL11-1
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.918370, 0.979440, 0.979035	SSRL	BL11-1

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	2.3	29.748	99.9	0.08	0.08	6.9	8.4		48701

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	2.3	2.36	98.7		0.602	0.602	1.3	5.5	3384

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	2.3	29.748	48668	2499	99.9	0.161	0.158	0.26	0.204	0.27	RANDOM	47.715

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]
1.34	0.67		1.34		-2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.011
r_dihedral_angle_4_deg	19.92
r_dihedral_angle_3_deg	15.966
r_dihedral_angle_1_deg	7.226
r_scangle_it	6.439
r_scbond_it	4.943
r_mcangle_it	2.592
r_mcbond_it	1.749
r_angle_refined_deg	1.572
r_angle_other_deg	0.985
r_mcbond_other	0.572
r_symmetry_vdw_refined	0.355
r_nbd_refined	0.211
r_nbd_other	0.191
r_nbtor_refined	0.179
r_symmetry_hbond_refined	0.158
r_symmetry_vdw_other	0.154
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.095
r_nbtor_other	0.09
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7174
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	40

Software

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