6BV6

Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana after 3-hour 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
2.957.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.738α = 90
b = 112.215β = 90
c = 139.206γ = 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
12.287.3698.90.05911.93.633697
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)
12.22.2798.40.5632.53.6

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 4G232.287.3631994164298.60.2070.2060.236RANDOM58.95
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]
-0.951.21-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.392
r_dihedral_angle_4_deg18.276
r_dihedral_angle_3_deg14.22
r_long_range_B_refined8.378
r_long_range_B_other8.335
r_scangle_other5.881
r_dihedral_angle_1_deg5.872
r_mcangle_it5.014
r_mcangle_other5.013
r_scbond_it3.589
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.392
r_dihedral_angle_4_deg18.276
r_dihedral_angle_3_deg14.22
r_long_range_B_refined8.378
r_long_range_B_other8.335
r_scangle_other5.881
r_dihedral_angle_1_deg5.872
r_mcangle_it5.014
r_mcangle_other5.013
r_scbond_it3.589
r_scbond_other3.588
r_mcbond_it3.233
r_mcbond_other3.233
r_angle_refined_deg1.374
r_angle_other_deg0.909
r_chiral_restr0.08
r_bond_refined_d0.011
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 Atoms3754
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing