1O9H

rRNA methyltransferase aviRa from Streptomyces viridochromogenes at 2.4A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.6MES 6.6,PEG 20K 11%, pH 6.60
Crystal Properties
Matthews coefficientSolvent content
2.1439

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.098α = 90
b = 48.937β = 99.05
c = 63.714γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287AREA DETECTORBRUKER2002-01-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.426.4900.07138.72.380392
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.46900.2823.21.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1O9G2.426.44770938290.10.2110.2090.241RANDOM49.48
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]
-2.64-0.552.77-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.981
r_scangle_it3.112
r_mcangle_it1.703
r_scbond_it1.66
r_angle_refined_deg1.188
r_mcbond_it0.912
r_angle_other_deg0.779
r_nbd_other0.218
r_symmetry_vdw_other0.214
r_nbd_refined0.196
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.981
r_scangle_it3.112
r_mcangle_it1.703
r_scbond_it1.66
r_angle_refined_deg1.188
r_mcbond_it0.912
r_angle_other_deg0.779
r_nbd_other0.218
r_symmetry_vdw_other0.214
r_nbd_refined0.196
r_xyhbond_nbd_refined0.175
r_symmetry_vdw_refined0.144
r_nbtor_other0.083
r_symmetry_hbond_refined0.065
r_chiral_restr0.061
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1868
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing