3ROD | pdb_00003rod

Methyltransferase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IIP	PDB ENTRY 2IIP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				25% PEG3350, 0.1 M BIS-TRIS; OR 25- 27% PEG3350, 0.2 M NACL, 0.1M BIS-TRIS OR IMIDAZOLE, PH 5.5 OR 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.663	α = 106.57
b = 61.793	β = 103.98
c = 74.342	γ = 104.14

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	CCD	ADSC QUANTUM 315	MIRRORS	2008-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

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	2.7	39.67	98.7	0.091	0.091	9.6	2.5		24960			57.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	97.5		1.9	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2IIP	2.72	39.67	23684	1272	98	0.208	0.205	0.2063	0.264	0.2622	RANDOM	36.96

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]
-1.78	0.09	0.94	1.43	0.75	1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.634
r_dihedral_angle_4_deg	22.878
r_dihedral_angle_3_deg	18.776
r_dihedral_angle_1_deg	5.332
r_mcangle_it	2.224
r_scangle_it	1.825
r_angle_refined_deg	1.678
r_mcbond_it	1.285
r_scbond_it	1.183
r_symmetry_vdw_refined	0.359
r_symmetry_hbond_refined	0.351
r_nbtor_refined	0.34
r_nbd_refined	0.292
r_xyhbond_nbd_refined	0.23
r_chiral_restr	0.095
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8082
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	140

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling