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Crystal Structure of Transcription Factor AXXA-PF0095 from Pyrococcus furiosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PLZ Pdb entry 2PLZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.8 291 70mM Sodium Acetate, 30% Glycerol, pH 4.8, modified microbatch, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 48.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.747 α = 90 b = 93.484 β = 102.44 c = 71.062 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 225 mm CCD 2007-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 32.53 98 0.058 6.6 11712
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.88 85 0.205 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 Pdb entry 2PLZ 2.8 32.53 11712 11712 608 98 0.246 0.244 0.2382 0.281 0.2681 RANDOM 79.95
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] -0.11 -0.2 0.39 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.775 r_dihedral_angle_4_deg 20.451 r_dihedral_angle_3_deg 17.482 r_dihedral_angle_1_deg 5.394 r_angle_refined_deg 1.058 r_scangle_it 0.915 r_mcangle_it 0.684 r_scbond_it 0.54 r_mcbond_it 0.378 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.775 r_dihedral_angle_4_deg 20.451 r_dihedral_angle_3_deg 17.482 r_dihedral_angle_1_deg 5.394 r_angle_refined_deg 1.058 r_scangle_it 0.915 r_mcangle_it 0.684 r_scbond_it 0.54 r_mcbond_it 0.378 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.069 r_symmetry_hbond_refined 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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 3324 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement SERGUI data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing