6BV9

Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana after overnight 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
2.8957.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.78α = 90
b = 111.818β = 90
c = 139.34γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16MK-B pair of biomorph mirrors for vertical and horizontal focusing2017-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

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
12.187.211000.05517.56.73912837
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)
12.12.1699.70.7172.26.5

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 4G232.187.213707819821000.1980.1960.241RANDOM63.12
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]
-0.231.54-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.389
r_dihedral_angle_4_deg17.785
r_dihedral_angle_3_deg14.963
r_long_range_B_refined8.457
r_long_range_B_other8.434
r_scangle_other6.153
r_dihedral_angle_1_deg6.12
r_mcangle_other5.489
r_mcangle_it5.486
r_scbond_it4.035
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.389
r_dihedral_angle_4_deg17.785
r_dihedral_angle_3_deg14.963
r_long_range_B_refined8.457
r_long_range_B_other8.434
r_scangle_other6.153
r_dihedral_angle_1_deg6.12
r_mcangle_other5.489
r_mcangle_it5.486
r_scbond_it4.035
r_scbond_other4.035
r_mcbond_it3.844
r_mcbond_other3.836
r_angle_refined_deg1.449
r_angle_other_deg0.921
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.007
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 Atoms3766
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing