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Structure of Caenorhabditis elegans leucine aminopeptidase (LAP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EWB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 100 MM MES, 2 M AMMONIUM SULFATE, PH 6.00, 5% GLYCEROL, 200 MM SODIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 58.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.82 α = 90 b = 131.82 β = 90 c = 125.573 γ = 120
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 RIGAKU RAXIS IV MIRRORS 2006-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 50 99.9 0.058 0.093 5.7 12.4 83359 83359
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.7 0.423 0.467 1.9 11.7 8253
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 2EWB 2 20 80790 80783 2492 99.93 0.1523 0.14845 0.1474 0.1512 0.18279 0.186 RANDOM 26.818
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] -0.15 -0.07 -0.15 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_4_deg 19.817 r_dihedral_angle_3_deg 14.67 r_scangle_it 7.393 r_dihedral_angle_1_deg 7.314 r_scbond_it 5.476 r_mcangle_it 3.809 r_mcbond_it 2.866 r_angle_refined_deg 1.248 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_4_deg 19.817 r_dihedral_angle_3_deg 14.67 r_scangle_it 7.393 r_dihedral_angle_1_deg 7.314 r_scbond_it 5.476 r_mcangle_it 3.809 r_mcbond_it 2.866 r_angle_refined_deg 1.248 r_nbtor_refined 0.302 r_metal_ion_refined 0.274 r_symmetry_hbond_refined 0.245 r_chiral_restr 0.218 r_xyhbond_nbd_refined 0.185 r_nbd_refined 0.183 r_symmetry_vdw_refined 0.171 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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_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 7330 Nucleic Acid Atoms Solvent Atoms 951 Heterogen Atoms 108
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement