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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 = 57.369 α = 90 b = 56.462 β = 93.74 c = 68.762 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 IMAGE PLATE MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A ESRF BM1A
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 13.71 99.2 0.115 4.5 4.9 45138
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 1.8 92.9 0.473 2 4.6
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 1.71 13.71 45138 2377 99.2 0.162 0.16 0.1727 0.202 0.2089 RANDOM 20.18
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] -0.79 -0.44 1.57 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.873 r_scangle_it 4.269 r_scbond_it 2.68 r_angle_refined_deg 1.972 r_mcangle_it 1.718 r_mcbond_it 1.029 r_angle_other_deg 0.979 r_symmetry_vdw_other 0.284 r_nbd_refined 0.253 r_nbd_other 0.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.873 r_scangle_it 4.269 r_scbond_it 2.68 r_angle_refined_deg 1.972 r_mcangle_it 1.718 r_mcbond_it 1.029 r_angle_other_deg 0.979 r_symmetry_vdw_other 0.284 r_nbd_refined 0.253 r_nbd_other 0.251 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.148 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.112 r_nbtor_other 0.091 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.002 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 3709 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling CNS phasing