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Crystal structure of phospholipase D from streptomyces antibioticus
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 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.004 α = 90 b = 85.008 β = 90 c = 99.343 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 FUJI mirrors 1997-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPring-8 BL41XU
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 2.5 100 90 0.056 14.1 2.9 19350 17415 26.2
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) 2.5 2.59 78.6 0.151 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIR THROUGHOUT 2.5 64.55 18600 15916 856 90.71 0.12374 0.12374 0.12111 0.1198 0.17101 0.1687 RANDOM 18.338
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] -0.16 1.19 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.624 r_dihedral_angle_4_deg 24.565 r_dihedral_angle_3_deg 17.006 r_dihedral_angle_1_deg 7.078 r_scangle_it 5.296 r_scbond_it 3.159 r_mcangle_it 1.942 r_angle_refined_deg 1.917 r_mcbond_it 1.144 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.624 r_dihedral_angle_4_deg 24.565 r_dihedral_angle_3_deg 17.006 r_dihedral_angle_1_deg 7.078 r_scangle_it 5.296 r_scbond_it 3.159 r_mcangle_it 1.942 r_angle_refined_deg 1.917 r_mcbond_it 1.144 r_nbtor_refined 0.313 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.125 r_symmetry_hbond_refined 0.117 r_chiral_restr 0.115 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3743 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Weissenberg data collection DENZO data reduction SCALEPACK data scaling MLPHARE phasing