357D

3.5 A structure of fragment I from E. coli 5S RRNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.4pH 6.40, VAPOR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
3.1459

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.67α = 90
b = 58.67β = 90
c = 248.84γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEFUJISILICON 111 BENDING MIRROR1996-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4ANSLSX4A

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
13.52099.10.0570.05711.34.96037-3-356.6
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)
3.53.6295.10.2910.2913.74.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMAD PHASES FROM A BROMINE WERE COMBINED WITH MAD AND SIRAS PHASES FROM A MERCURY DERIVIATIVE. MLPHARE WAS USED TO CALCULATE THE PHASES WHILE SIGMAA WAS USED TO COMBINE THE THREE PHASES SETS.THROUGHOUT3.510337437297.40.3120.3120.265RANDOM98.6
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]
6.0532.876.05-12
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d29.9
c_improper_angle_d2.63
c_mcangle_it2.34
c_scangle_it1.64
c_angle_deg1.5
c_mcbond_it1.35
c_scbond_it0.98
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d29.9
c_improper_angle_d2.63
c_mcangle_it2.34
c_scangle_it1.64
c_angle_deg1.5
c_mcbond_it1.35
c_scbond_it0.98
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms1294
Solvent Atoms
Heterogen Atoms9

Software

Software
Software NamePurpose
CCP4model building
X-PLOR/CNSmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
X-PLORphasing
CNSphasing