3Q22

X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with GTP and Magnesium: substrate complex I


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82940.1 M TRIS-HCL, 0.21 M DIBASIC AMMONIUM CITRATE, 0.09 M AMMONIUM DIHYDROGEN MONOPHOSPHATE, 25 % (DROP) 15% (RESERVOIR) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.448.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.3α = 90
b = 111.787β = 90
c = 276.85γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

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
12.15089.70.0910.23.313345713345711
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)
12.12.18730.6142.8

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1150126713133426671389.10.2090.2080.219RANDOM30.91
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]
1.49-0.59-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.492
r_dihedral_angle_3_deg15.744
r_dihedral_angle_4_deg15.252
r_dihedral_angle_1_deg4.906
r_scangle_it1.915
r_scbond_it1.149
r_angle_refined_deg1.117
r_mcangle_it0.848
r_mcbond_it0.495
r_nbtor_refined0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.492
r_dihedral_angle_3_deg15.744
r_dihedral_angle_4_deg15.252
r_dihedral_angle_1_deg4.906
r_scangle_it1.915
r_scbond_it1.149
r_angle_refined_deg1.117
r_mcangle_it0.848
r_mcbond_it0.495
r_nbtor_refined0.29
r_symmetry_hbond_refined0.225
r_nbd_refined0.179
r_symmetry_vdw_refined0.165
r_xyhbond_nbd_refined0.155
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16897
Nucleic Acid Atoms828
Solvent Atoms1420
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing