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Crystal structure of Pseudomonas sp. MIS38 lipase (PML) in the open conformation following dialysis against Ca-free buffer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZVD PDB ENTRY 2ZVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.1M Tris-HCl, pH8.5, 0.2M ammonium acetate, 30% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.02 59.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.382 α = 90 b = 104.382 β = 90 c = 495.175 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 2009-02-27 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 2.15 50 99.3 0.136 0.109 13.76 6.9 87709
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) 2.15 2.23 99.2 0.437 3.1 5.6 8579
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2ZVD 2.15 48.11 83266 4397 99.45 0.18431 0.18244 0.1839 0.21965 0.2201 RANDOM 21.34
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.304 r_dihedral_angle_4_deg 22.138 r_dihedral_angle_3_deg 15.402 r_dihedral_angle_1_deg 7.276 r_scangle_it 3.61 r_scbond_it 2.542 r_angle_refined_deg 1.724 r_mcangle_it 1.573 r_mcbond_it 0.977 r_symmetry_hbond_refined 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.304 r_dihedral_angle_4_deg 22.138 r_dihedral_angle_3_deg 15.402 r_dihedral_angle_1_deg 7.276 r_scangle_it 3.61 r_scbond_it 2.542 r_angle_refined_deg 1.724 r_mcangle_it 1.573 r_mcbond_it 0.977 r_symmetry_hbond_refined 0.51 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.276 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.122 r_metal_ion_refined 0.099 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9078 Nucleic Acid Atoms Solvent Atoms 631 Heterogen Atoms 17
Software Software Software Name Purpose BL44XU data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling