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Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZE4 PDB ENTRY 2ZE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 15% PEG 6000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.17 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.868 α = 90 b = 78.232 β = 90 c = 98.603 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU RAXIS IV mirrors 1999-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.3 61.31 97 0.07 17.2 3.4 21448 20805 23.6
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) 2.3 2.42 88.8 0.157 5.5 2.2 2726
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2ZE4 2.3 48.04 21555 19582 1071 95.84 0.17448 0.17448 0.17029 0.1739 0.25137 0.1804 RANDOM 13.618
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] -0.21 0.5 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.105 r_dihedral_angle_4_deg 22.262 r_dihedral_angle_3_deg 15.629 r_dihedral_angle_1_deg 8.218 r_scangle_it 3.584 r_scbond_it 2.329 r_angle_refined_deg 1.894 r_mcangle_it 1.512 r_mcbond_it 0.928 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.105 r_dihedral_angle_4_deg 22.262 r_dihedral_angle_3_deg 15.629 r_dihedral_angle_1_deg 8.218 r_scangle_it 3.584 r_scbond_it 2.329 r_angle_refined_deg 1.894 r_mcangle_it 1.512 r_mcbond_it 0.928 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.225 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.207 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3758 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALA data scaling MOLREP phasing