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Crystal structure of transcription regulator CcpA of Lactococcus lactis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZVV PDB ENTRY 1ZVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 296 PEG 3350 (22.5% (w/v), 100 mM Li2SO4, 100 mM Tris/HCl, VAPOR DIFFUSION, HANGING DROP, temperature 296K, pH 8.00
Crystal Properties Matthews coefficient Solvent content 2.34 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.756 α = 90 b = 74.267 β = 102.36 c = 160.302 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 ADSC QUANTUM 4 2005-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.9 19.9 99.4 11.74 5.5 211799
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 99.1 4.49 4.4
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 1ZVV 1.9 19.9 211799 201126 10565 99.4 0.177 0.176 0.1848 0.211 0.2174 RANDOM 29.7
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] 0.83 0.41 0.18 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.66 r_dihedral_angle_4_deg 19.107 r_dihedral_angle_3_deg 13.91 r_dihedral_angle_1_deg 5.84 r_scangle_it 3.14 r_scbond_it 1.984 r_angle_refined_deg 1.289 r_mcangle_it 1.253 r_angle_other_deg 0.808 r_mcbond_it 0.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.66 r_dihedral_angle_4_deg 19.107 r_dihedral_angle_3_deg 13.91 r_dihedral_angle_1_deg 5.84 r_scangle_it 3.14 r_scbond_it 1.984 r_angle_refined_deg 1.289 r_mcangle_it 1.253 r_angle_other_deg 0.808 r_mcbond_it 0.808 r_symmetry_vdw_refined 0.207 r_symmetry_vdw_other 0.2 r_nbd_refined 0.197 r_mcbond_other 0.194 r_nbd_other 0.167 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_other 0.114 r_nbtor_other 0.079 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16891 Nucleic Acid Atoms Solvent Atoms 1335 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing