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X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with GTP and Magnesium: substrate complex I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 0.1 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 coefficient Solvent content 2.4 48.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.3 α = 90 b = 111.787 β = 90 c = 276.85 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2005-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 50 89.7 0.09 10.2 3.3 133457 133457 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 73 0.614 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.11 50 126713 133426 6713 89.1 0.209 0.208 0.2083 0.219 0.2196 RANDOM 30.91
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.492 r_dihedral_angle_3_deg 15.744 r_dihedral_angle_4_deg 15.252 r_dihedral_angle_1_deg 4.906 r_scangle_it 1.915 r_scbond_it 1.149 r_angle_refined_deg 1.117 r_mcangle_it 0.848 r_mcbond_it 0.495 r_nbtor_refined 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.492 r_dihedral_angle_3_deg 15.744 r_dihedral_angle_4_deg 15.252 r_dihedral_angle_1_deg 4.906 r_scangle_it 1.915 r_scbond_it 1.149 r_angle_refined_deg 1.117 r_mcangle_it 0.848 r_mcbond_it 0.495 r_nbtor_refined 0.29 r_symmetry_hbond_refined 0.225 r_nbd_refined 0.179 r_symmetry_vdw_refined 0.165 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 Atoms Number Protein Atoms 16897 Nucleic Acid Atoms 828 Solvent Atoms 1420 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement CNS refinement CBASS data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing