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Crystal Structure of the Lambda Repressor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LMB 1LMB, 1F39 experimental model PDB 1F39 1LMB, 1F39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 294 14% PEG 4000, 0.1 M Sodium Acetate pH 4.6, 0.2 M Ammonium Sulfate, 0.05 M Magnesium Chloride, 20% Glycerol, 1 mM Spermine, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.15 60.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.431 α = 90 b = 161.099 β = 90 c = 135.256 γ = 90
Symmetry Space Group C 2 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 CCD ADSC QUANTUM 315 2002-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0 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 3.909 34.61 99 0.048 21.2 10 7810 7238 111
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) 3.909 4.14 100 0.176 8 9.2 629
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1LMB, 1F39 3.909 34.61 7238 7238 350 98.92 0.29597 0.29597 0.29211 0.37413 RANDOM 170.2
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] -0.14 0.89 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.503 r_dihedral_angle_1_deg 9.183 r_angle_refined_deg 1.773 r_scangle_it 1.523 r_scbond_it 1.166 r_mcangle_it 1.135 r_mcbond_it 0.701 r_symmetry_vdw_refined 0.306 r_nbd_refined 0.304 r_symmetry_hbond_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.503 r_dihedral_angle_1_deg 9.183 r_angle_refined_deg 1.773 r_scangle_it 1.523 r_scbond_it 1.166 r_mcangle_it 1.135 r_mcbond_it 0.701 r_symmetry_vdw_refined 0.306 r_nbd_refined 0.304 r_symmetry_hbond_refined 0.295 r_xyhbond_nbd_refined 0.259 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3626 Nucleic Acid Atoms 779 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CBASS data collection MLPHARE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling