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Phospholipase D from Streptomyces sp. strain PMF soaked with the substrate dibutyrylphosphatidylcholine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F0I BASED ON PDB ENTRY 1F0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.4 0.2 M NH4AC, 0.1 M CITRATE PHOSPHATE BUFFER AT PH5.4, 27.5% PEG 4000. CRYSTALS WERE THEREAFTER BACKSOAKED TWICE IN A PHOSPHATE- FREE BUFFER TO REMOVE TRACE-AMOUNTS OF PHOSPHATE., pH 5.40
Crystal Properties Matthews coefficient Solvent content 2 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.45 α = 90 b = 56.75 β = 93.39 c = 68.54 γ = 90
Symmetry Space Group P 1 21 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.7 69.01 90.7 0.064 6.5 3.3 41858
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) 1 1.7 1.79 64.1 0.136 4.9 1.7
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 BASED ON PDB ENTRY 1F0I 1.7 69.01 41858 2229 90.7 0.164 0.162 0.1728 0.208 0.2191 RANDOM 17.98
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] -1.46 -1.06 0.1 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.924 r_scangle_it 4.117 r_scbond_it 2.678 r_angle_refined_deg 2 r_mcangle_it 1.816 r_mcbond_it 1.093 r_angle_other_deg 0.986 r_nbd_refined 0.25 r_nbd_other 0.25 r_symmetry_vdw_other 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.924 r_scangle_it 4.117 r_scbond_it 2.678 r_angle_refined_deg 2 r_mcangle_it 1.816 r_mcbond_it 1.093 r_angle_other_deg 0.986 r_nbd_refined 0.25 r_nbd_other 0.25 r_symmetry_vdw_other 0.233 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.124 r_symmetry_vdw_refined 0.11 r_chiral_restr 0.109 r_nbtor_other 0.092 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.011 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3704 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling CNS phasing