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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 = 57.227 α = 90 b = 56.37 β = 93.69 c = 68.631 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 120 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 1.35 19.5 99 0.05 8.5 4.7 89964
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 1.35 1.42 99.7 0.344 2 4.5
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 1.35 19.5 89964 4771 99 0.162 0.161 0.1735 0.186 0.1993 RANDOM 13.41
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] -0.62 -0.26 0.55 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.646 r_scangle_it 2.982 r_angle_refined_deg 1.95 r_scbond_it 1.896 r_mcangle_it 1.299 r_angle_other_deg 0.946 r_mcbond_it 0.736 r_nbd_refined 0.255 r_nbd_other 0.25 r_symmetry_vdw_other 0.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.646 r_scangle_it 2.982 r_angle_refined_deg 1.95 r_scbond_it 1.896 r_mcangle_it 1.299 r_angle_other_deg 0.946 r_mcbond_it 0.736 r_nbd_refined 0.255 r_nbd_other 0.25 r_symmetry_vdw_other 0.224 r_symmetry_hbond_refined 0.216 r_xyhbond_nbd_refined 0.154 r_symmetry_vdw_refined 0.1 r_nbtor_other 0.095 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 3735 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling CNS phasing