3WYZ

On archaeal homologs of the human RNase P protein Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Purification7.528350mM Tris-HCl (pH 7.5), 200mM NaCl, 10mM MgCl2, Purification, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
1.9235.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.61α = 90
b = 58.725β = 109.67
c = 43.28γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HEMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
12.25096.80.14118.43.294229422
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)
12.22.393.50.9172.73

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.2133.488799879943194.630.221910.221910.219010.28136RANDOM56.06
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]
-0.010.04-0.040.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.083
r_dihedral_angle_3_deg14.138
r_dihedral_angle_4_deg13.973
r_long_range_B_refined7.223
r_long_range_B_other7.223
r_dihedral_angle_1_deg5.043
r_scangle_other3.7
r_mcangle_it3.268
r_mcangle_other3.267
r_scbond_it2.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.083
r_dihedral_angle_3_deg14.138
r_dihedral_angle_4_deg13.973
r_long_range_B_refined7.223
r_long_range_B_other7.223
r_dihedral_angle_1_deg5.043
r_scangle_other3.7
r_mcangle_it3.268
r_mcangle_other3.267
r_scbond_it2.222
r_scbond_other2.222
r_mcbond_it1.971
r_mcbond_other1.971
r_angle_refined_deg0.939
r_angle_other_deg0.686
r_chiral_restr0.05
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1717
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms6

Software

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