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X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with GMPCPP and Manganese: sustrate complex II
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) 20% (RESERVOIR) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.38 48.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.834 α = 90 b = 111.861 β = 90 c = 276.093 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 2006-11-10 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 1.8 50 99 0.064 10.5 6 234419 234419 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) 1.8 1.86 91.5 0.545 4.4
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 (All) 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 1.8 50 234301 234301 11758 99 0.201 0.201 0.2 0.1984 0.231 0.2303 RANDOM 28
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] 0.99 -0.5 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.603 r_dihedral_angle_4_deg 16.038 r_dihedral_angle_3_deg 15.076 r_dihedral_angle_1_deg 4.8 r_scangle_it 1.843 r_scbond_it 1.163 r_angle_refined_deg 1.066 r_mcangle_it 0.819 r_mcbond_it 0.606 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.603 r_dihedral_angle_4_deg 16.038 r_dihedral_angle_3_deg 15.076 r_dihedral_angle_1_deg 4.8 r_scangle_it 1.843 r_scbond_it 1.163 r_angle_refined_deg 1.066 r_mcangle_it 0.819 r_mcbond_it 0.606 r_nbtor_refined 0.294 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.103 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.07 r_bond_refined_d 0.007 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 2626 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement CNS refinement CBASS data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing