3SPA

Crystal Structure of Human Mitochondrial RNA Polymerase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QLNPDB entry 1QLN, truncated to polyAlanine, residues 246-354, 392-568, 691-741, 766-883 of model used

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529312% PEG4000, 10% Glycerol, 30mM Mes 6.5, 60mM (NH4)2SO4, 40mM Tris 8.0, 20mM DTT in situ proteolysed with ArgC (1:1000 w/w ratio) and micro-seeded, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 211.258α = 90
b = 211.258β = 90
c = 60.461γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray63CCDMARMOSAIC 225 mm CCD2011-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0000SLSX06DA

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
12.558.1280.04715.93.8465954650773.16
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)
12.52.640.6311.93.86694

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB entry 1QLN, truncated to polyAlanine, residues 246-354, 392-568, 691-741, 766-883 of model used2.558.1284650746505237899.810.18780.18780.18550.231RANDOM89.21
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]
9.35669.3566-18.7131
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion19.41
t_omega_torsion2.6
o_angle_deg1.12
o_bond_d0.009
o_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7457
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms22

Software

Software
Software NamePurpose
PHASERphasing
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling