3ASM

Crystal structure of Q54A mutant protein of Bst-RNase HIII


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D0APDB ENTRY 2D0A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.085M Tris-HCl pH 8.5, 0.17M lithium sulfate, 25.5% PEG 4000, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6253.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.249α = 90
b = 109.106β = 90
c = 48.329γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210mirrors2008-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11SPring-8BL38B1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.65099.90.1060.08618.56.91144555
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)RedundancyNumber Unique Reflections (All)
12.62.6998.90.40.3553.335.41102

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 2D0A2.60344.19114131086754699.890.204980.203640.23262RANDOM25.873
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.511
r_dihedral_angle_4_deg21.969
r_dihedral_angle_3_deg21.95
r_dihedral_angle_1_deg8.448
r_scangle_it5.813
r_scbond_it3.817
r_mcangle_it2.38
r_mcbond_it1.301
r_angle_refined_deg0.925
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.511
r_dihedral_angle_4_deg21.969
r_dihedral_angle_3_deg21.95
r_dihedral_angle_1_deg8.448
r_scangle_it5.813
r_scbond_it3.817
r_mcangle_it2.38
r_mcbond_it1.301
r_angle_refined_deg0.925
r_chiral_restr0.076
r_gen_planes_refined0.015
r_bond_refined_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2359
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms

Software

Software
Software NamePurpose
BL38data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling