3Q24

X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with pppGpG and pyrophosphate: product complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1HANGING DROP82940.1 M TRIS-HCL, 0.21 M DIBASIC AMMONIUM CITRATE, 0.09 M AMMONIUM DIHYDROGEN MONOPHOSPHATE, 25% (DROP) 21.5-22% (RESERVOIR) PEG 3350, pH 8.0, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.4148.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.459α = 90
b = 111.79β = 90
c = 277.009γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-11-10MSINGLE 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
11.85099.70.07210.55.923349323349311
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)
1.81.8698.70.7284.2

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 REPLACEMENTTHROUGHOUT1.8141.492333622333621169898.90.2020.2020.2010.235RANDOM32.61
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]
1.03-0.14-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.062
r_dihedral_angle_4_deg16.76
r_dihedral_angle_3_deg14.905
r_dihedral_angle_1_deg5.187
r_scangle_it2.152
r_scbond_it1.401
r_angle_refined_deg1.096
r_mcangle_it0.94
r_mcbond_it0.726
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.062
r_dihedral_angle_4_deg16.76
r_dihedral_angle_3_deg14.905
r_dihedral_angle_1_deg5.187
r_scangle_it2.152
r_scbond_it1.401
r_angle_refined_deg1.096
r_mcangle_it0.94
r_mcbond_it0.726
r_nbtor_refined0.296
r_symmetry_vdw_refined0.194
r_nbd_refined0.19
r_xyhbond_nbd_refined0.112
r_symmetry_hbond_refined0.11
r_chiral_restr0.075
r_bond_refined_d0.007
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 Atoms881
Solvent Atoms2399
Heterogen Atoms83

Software

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