6BV5

Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana after 45-minute soak with juglone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4G23PDB ENTRY 4G23

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.527718% PEG3350, 0.1 M sodium citrate tribasic, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.8757.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.616α = 90
b = 110.838β = 90
c = 140.743γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MK-B pair of biomorph mirrors for vertical and horizontal focusing2017-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033200APS23-ID-D

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
11.7987.0899.10.03615.93.761385
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)
11.791.8396.30.4781.93.6

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 4G231.7987.0857980303398.40.1970.1960.223RANDOM48.74
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]
-0.411.09-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.459
r_dihedral_angle_4_deg18.231
r_dihedral_angle_3_deg12.37
r_long_range_B_refined6.369
r_long_range_B_other6.315
r_dihedral_angle_1_deg5.582
r_scangle_other4.731
r_mcangle_it3.573
r_mcangle_other3.572
r_scbond_it2.922
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.459
r_dihedral_angle_4_deg18.231
r_dihedral_angle_3_deg12.37
r_long_range_B_refined6.369
r_long_range_B_other6.315
r_dihedral_angle_1_deg5.582
r_scangle_other4.731
r_mcangle_it3.573
r_mcangle_other3.572
r_scbond_it2.922
r_scbond_other2.921
r_mcbond_it2.469
r_mcbond_other2.465
r_angle_refined_deg1.284
r_angle_other_deg0.893
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3767
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing