2ZFU | pdb_00002zfu

Structure of the methyltransferase-like domain of nucleomethylin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	30% PEG 8000, 200mM Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.81	α = 90
b = 43.81	β = 90
c = 403.91	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 315		2006-04-09	M	SINGLE WAVELENGTH
2	1	x-ray	93	CCD	ADSC QUANTUM 315		2006-03-05	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	0.97912,0.97931,0.96408	Photon Factory	BL-5A

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	2	67.27	98	0.072		11	28996	28996

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	2	2.07	92		0.284		3.4

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	36.52	27381	1467	98.27	0.19361	0.19161	0.2	0.23066	0.24	RANDOM	30.008

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]
0.36	0.18		0.36		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.908
r_dihedral_angle_4_deg	16.5
r_dihedral_angle_3_deg	14.977
r_dihedral_angle_1_deg	5.903
r_scangle_it	2.097
r_scbond_it	1.446
r_angle_refined_deg	1.237
r_angle_other_deg	0.86
r_mcangle_it	0.802
r_mcbond_it	0.725
r_symmetry_vdw_other	0.256
r_nbd_refined	0.207
r_nbd_other	0.189
r_symmetry_hbond_refined	0.18
r_nbtor_refined	0.179
r_xyhbond_nbd_other	0.177
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.15
r_mcbond_other	0.114
r_nbtor_other	0.085
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3299
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing