3ZWF

Crystal structure of Human tRNase Z, short form (ELAC1).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherMODEL DETERMINED FROM SIRAS EXPERIMENT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1715% PEG 3350 0.2M NA NITRATE, pH 7
Crystal Properties
Matthews coefficientSolvent content
238.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.52α = 90
b = 73.79β = 98.69
c = 73.66γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2011-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.749.57970.048.83.46711127.82
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)
11.71.7995.30.0423.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTMODEL DETERMINED FROM SIRAS EXPERIMENT1.772.8163620340096.660.187760.186560.190.210150.21RANDOM27.713
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]
0.320.9-0.240.19
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.212
r_sphericity_bonded42.796
r_dihedral_angle_2_deg35.555
r_dihedral_angle_4_deg24.702
r_dihedral_angle_3_deg11.776
r_dihedral_angle_1_deg5.705
r_angle_refined_deg1.49
r_angle_other_deg1.27
r_chiral_restr0.093
r_bond_refined_d0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3903
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing