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Structure of transcription regulator CcpA in its DNA-free state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SXH pdb entry 1SXH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 3% polyethylene glycol 8000, 100mM CaCl2, 10% (v/v) glycerol, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.61 52.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.464 α = 90 b = 74.464 β = 90 c = 238.923 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 1997-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.95 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 30 98.4 14394 14158 66.898
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) 2.5 2.565 96.1 0.436 3.7
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 (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 pdb entry 1SXH 2.5 30 13447 14158 711 98.26 0.275 0.281 0.271 0.2705 0.337 0.3428 RANDOM 58.514
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] 1.36 0.68 1.36 -2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.646 r_dihedral_angle_4_deg 21.272 r_dihedral_angle_3_deg 18.675 r_dihedral_angle_1_deg 8.653 r_mcangle_it 2.191 r_angle_refined_deg 1.616 r_scangle_it 1.551 r_mcbond_it 1.344 r_scbond_it 0.998 r_angle_other_deg 0.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.646 r_dihedral_angle_4_deg 21.272 r_dihedral_angle_3_deg 18.675 r_dihedral_angle_1_deg 8.653 r_mcangle_it 2.191 r_angle_refined_deg 1.616 r_scangle_it 1.551 r_mcbond_it 1.344 r_scbond_it 0.998 r_angle_other_deg 0.809 r_symmetry_vdw_refined 0.36 r_symmetry_vdw_other 0.31 r_nbd_refined 0.279 r_nbd_other 0.237 r_xyhbond_nbd_refined 0.228 r_symmetry_hbond_refined 0.222 r_mcbond_other 0.222 r_chiral_restr 0.118 r_nbtor_other 0.097 r_xyhbond_nbd_other 0.086 r_gen_planes_refined 0.015 r_bond_refined_d 0.014 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2506 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling PHASER phasing