2QG3 | pdb_00002qg3

CRYSTAL STRUCTURE OF A TYW3 METHYLTRANSFERASE-LIKE PROTEIN (AF_2059) FROM ARCHAEOGLOBUS FULGIDUS DSM 4304 AT 1.95 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	NANODROP, 0.09M Citric acid, 0.01M Trisodium citrate, 20% MPD, Additive: 0.01 M Phenol, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 4.0
2	VAPOR DIFFUSION, SITTING DROP	4.1	293	NANODROP, 0.08M Citric acid, 0.02M Trisodium citrate, 22% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 4.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.334	α = 90
b = 59.334	β = 90
c = 109.102	γ = 90

Symmetry
Space Group	P 42

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	ADSC QUANTUM 315	Flat collimating mirror, toroid focusing mirror	2004-07-31	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC QUANTUM 315	Flat mirror (vertical focusing)	2004-07-05	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979105	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.885567, 0.979508, 0.979224	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	1.95	28.628	99.8	0.088	0.088	7.5	3.7		27454			24.94

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	1.95	2.06	99.8		0.756	0.756	1	3.8	3997

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	1.95	28.628	27438	1377	99.77	0.201	0.199	0.21	0.253	0.26	RANDOM	25.35

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]
1.41			1.41		-2.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.5
r_dihedral_angle_4_deg	20.398
r_dihedral_angle_3_deg	14.935
r_scangle_it	8.115
r_dihedral_angle_1_deg	6.561
r_scbond_it	5.868
r_mcangle_it	3.498
r_mcbond_it	2.309
r_angle_refined_deg	1.495
r_angle_other_deg	0.825
r_mcbond_other	0.553
r_nbd_refined	0.211
r_symmetry_vdw_other	0.184
r_nbtor_refined	0.181
r_nbd_other	0.162
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.125
r_symmetry_vdw_refined	0.104
r_nbtor_other	0.09
r_chiral_restr	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2876
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
XSCALE	data scaling
PDB_EXTRACT	data extraction
SHARP	phasing
Blu-Ice	data collection
XDS	data reduction
SHELXD	phasing