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Crystal structure of Pseudomonas sp. MIS38 lipase in an open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z8X PDB ENTRY 2Z8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2M ammonium acetate, 0.1M Tris-HCl, pH8.5, 30% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 3.06 59.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.781 α = 90 b = 104.781 β = 90 c = 497.926 γ = 120
Symmetry Space Group P 65 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 Bruker DIP-6040 mirrors 2008-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.0 SPring-8 BL44XU
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 2.1 40 100 0.103 0.077 27.7 10.9 171224 95813
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) 2.1 2.18 100 0.406 0.401 6.3 11 9353
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Z8X 2.15 40 84781 4473 99.99 0.172 0.17001 0.20979 0.2037 RANDOM 22.724
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.611 r_dihedral_angle_4_deg 20.081 r_dihedral_angle_3_deg 15.097 r_dihedral_angle_1_deg 7.287 r_scangle_it 3.883 r_scbond_it 2.538 r_angle_refined_deg 1.585 r_mcangle_it 1.555 r_mcbond_it 0.906 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.611 r_dihedral_angle_4_deg 20.081 r_dihedral_angle_3_deg 15.097 r_dihedral_angle_1_deg 7.287 r_scangle_it 3.883 r_scbond_it 2.538 r_angle_refined_deg 1.585 r_mcangle_it 1.555 r_mcbond_it 0.906 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.221 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.201 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.115 r_metal_ion_refined 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9037 Nucleic Acid Atoms Solvent Atoms 1228 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement SPring data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing