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Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R1J PDB entry 2R1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 277 PEG 400, NaCl, Tris-HCl, MgCl2, LiCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.602 α = 90 b = 54.319 β = 90 c = 114.112 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 110 CCD ADSC QUANTUM 4 2007-08-13 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.000 NSLS X26C
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 1.67 19.9 97.26 0.069 47.1 5.8 29254 29254
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 1.67 1.71 91.7 0.659 2.12 4.7 2003
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2R1J 1.67 19.9 1 27753 1501 97.26 0.198 0.196 0.1899 0.226 0.2172 RANDOM 19.389
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] -0.02 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.738 r_dihedral_angle_3_deg 12.655 r_dihedral_angle_4_deg 7.156 r_dihedral_angle_1_deg 5.318 r_scangle_it 1.979 r_angle_refined_deg 1.621 r_scbond_it 1.357 r_mcangle_it 0.882 r_mcbond_it 0.623 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.738 r_dihedral_angle_3_deg 12.655 r_dihedral_angle_4_deg 7.156 r_dihedral_angle_1_deg 5.318 r_scangle_it 1.979 r_angle_refined_deg 1.621 r_scbond_it 1.357 r_mcangle_it 0.882 r_mcbond_it 0.623 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.109 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1031 Nucleic Acid Atoms 814 Solvent Atoms 300 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing