2R8S

High resolution structure of a specific synthetic FAB bound to P4-P6 RNA ribozyme domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TZIPDB ENTRY 1TZI 1HR2
experimental modelPDB 1HR2PDB ENTRY 1TZI 1HR2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.927734% MPD, 0.1M sodium citrate, 0.2M ammonium acetate, 25 mM magnesium chloride, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7455.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.085α = 90
b = 53.23β = 108.42
c = 160.555γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-2mirrors2006-05-29MSINGLE WAVELENGTH
21x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2006-06-05MSINGLE WAVELENGTH
31x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2006-06-15MSINGLE WAVELENGTH
1,2,31
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM
2SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D
3SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

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
1,2,31.952098.60.08816.75.27712777127
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)
1,2,31.95295.50.481.62.7

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1TZI 1HR21.95207712777127387598.60.196320.196320.194760.22607RANDOM35.918
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]
-2.23-0.40.941.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.954
r_dihedral_angle_4_deg14.991
r_dihedral_angle_3_deg14.124
r_dihedral_angle_1_deg7.445
r_scangle_it3.183
r_scbond_it2.349
r_mcangle_it2.092
r_angle_refined_deg1.33
r_mcbond_it1.271
r_angle_other_deg1.022
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.954
r_dihedral_angle_4_deg14.991
r_dihedral_angle_3_deg14.124
r_dihedral_angle_1_deg7.445
r_scangle_it3.183
r_scbond_it2.349
r_mcangle_it2.092
r_angle_refined_deg1.33
r_mcbond_it1.271
r_angle_other_deg1.022
r_mcbond_other0.326
r_nbtor_refined0.212
r_nbd_other0.205
r_symmetry_vdw_other0.183
r_nbd_refined0.162
r_symmetry_vdw_refined0.151
r_xyhbond_nbd_refined0.147
r_symmetry_hbond_refined0.141
r_nbtor_other0.08
r_chiral_restr0.059
r_metal_ion_refined0.038
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3263
Nucleic Acid Atoms3404
Solvent Atoms529
Heterogen Atoms4

Software

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