2A2E

Crystal structure of the RNA subunit of Ribonuclease P. Bacterial A-type.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U9SPDB ENTRY 1U9S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.530325% MPD, 200 mM KCl, 5 mM SrCl2, 50 mM MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Crystal Properties
Matthews coefficientSolvent content
3.460

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 179.277α = 90
b = 85.231β = 96.83
c = 101.912γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrors2004-11-11MSINGLE WAVELENGTH
21x-ray100CCDMARRESEARCHmirrors2004-11-11MSINGLE WAVELENGTH
31x-ray100CCDMARRESEARCHmirrors2004-11-11MSINGLE WAVELENGTH
41x-ray100CCDmarccdmirrors2004-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 5ID-BAPS5ID-B
2SYNCHROTRONAPS BEAMLINE 5ID-BAPS5ID-B
3SYNCHROTRONAPS BEAMLINE 5ID-BAPS5ID-B
4SYNCHROTRONAPS BEAMLINE 5ID-BAPS5ID-B

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
1,2,3,43.8521.0597.20.060.0611.52.7143281392711
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)
1,2,3,43.853.9598.998.90.2310.2312.82.61046

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUTPDB ENTRY 1U9S3.8582129801265260297.50.3630.3560.34410.3617RANDOM81.165
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]
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18
c_improper_angle_d2.14
c_angle_deg1.87
c_bond_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms5758
Solvent Atoms
Heterogen Atoms17

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
SHARPphasing
SOLOMONphasing
CNSrefinement
PDB_EXTRACTdata extraction
CCP4data scaling