6BV8

Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana complexed with Mn after 3-hour soak with juglone


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.527718% PEG3350, 0.1 M sodium citrate tribasic, pH 5.5
Crystal Properties
Matthew coefficientSolvent content
2.8757.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.677α = 90
b = 111.332β = 90
c = 139.389γ = 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 focusing2017-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033100APS23-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
12.186.9999.20.04813.43.53850038
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)
12.12.1697.90.6361.63.4

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 4G232.186.9936554190098.720.202220.20040.23608RANDOM54.091
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]
-0.21.78-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.763
r_dihedral_angle_4_deg17.874
r_dihedral_angle_3_deg13.61
r_long_range_B_refined7.286
r_long_range_B_other7.184
r_dihedral_angle_1_deg5.833
r_scangle_other5.248
r_mcangle_it4.27
r_mcangle_other4.269
r_scbond_it3.345
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.763
r_dihedral_angle_4_deg17.874
r_dihedral_angle_3_deg13.61
r_long_range_B_refined7.286
r_long_range_B_other7.184
r_dihedral_angle_1_deg5.833
r_scangle_other5.248
r_mcangle_it4.27
r_mcangle_other4.269
r_scbond_it3.345
r_scbond_other3.345
r_mcbond_it2.863
r_mcbond_other2.86
r_angle_refined_deg1.312
r_angle_other_deg0.901
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.001
r_bond_other_d0.001
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3767
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing