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Open conformation of Burkholderia stagnalis lipase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 277 0.1 M HEPES, pH 7.0, 45% MPD, 1 M ammonium fluoride, 3% methanol
Crystal Properties Matthews coefficient Solvent content 1.88 34.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.643 α = 90 b = 69.21 β = 98.531 c = 51.322 γ = 90
Symmetry Space Group C 1 2 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 270 2018-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.399 50 99.8 0.996 24.5 3.6 109236
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.399 1.42 99.9 0.835 0.627 1.8 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.399 29.243 109215 5565 99.666 0.163 0.163 0.162 0.162 0.1838 0.1838 14.617
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] 0.001 0.001 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.559 r_dihedral_angle_3_deg 9.793 r_dihedral_angle_1_deg 6.122 r_dihedral_angle_2_deg 4.802 r_lrange_it 3.474 r_lrange_other 3.075 r_scangle_it 1.795 r_scangle_other 1.795 r_angle_refined_deg 1.19 r_scbond_it 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.559 r_dihedral_angle_3_deg 9.793 r_dihedral_angle_1_deg 6.122 r_dihedral_angle_2_deg 4.802 r_lrange_it 3.474 r_lrange_other 3.075 r_scangle_it 1.795 r_scangle_other 1.795 r_angle_refined_deg 1.19 r_scbond_it 1.12 r_scbond_other 1.119 r_mcangle_it 1.015 r_mcangle_other 1.015 r_mcbond_it 0.642 r_mcbond_other 0.642 r_angle_other_deg 0.441 r_nbd_other 0.228 r_nbd_refined 0.213 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.155 r_xyhbond_nbd_refined 0.108 r_symmetry_nbtor_other 0.079 r_metal_ion_refined 0.076 r_chiral_restr 0.062 r_symmetry_xyhbond_nbd_other 0.006 r_gen_planes_refined 0.005 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4682 Nucleic Acid Atoms Solvent Atoms 601 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing