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Crystal structure of Zucchini from mouse (mZuc / PLD6 / MitoPLD) bound to tungstate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BYR PDB entry 1BYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 50 mM Bis-Tris, pH 6.5, 18% PEG-3350, 2% tascimate, pH 6.0, 1:100 m/m ratio protein:chymotrypsin, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.8 31.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.859 α = 90 b = 38.859 β = 90 c = 213.31 γ = 90
Symmetry Space Group P 43 21 2
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 QUANTUM 315 2012-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.2716, 1.2983 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 40 99.5 18.3 5.8 10188 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.23 98.1 5.6 5.8 2879
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 1BYR 2.1 38.27 9676 9676 514 99.43 0.21144 0.21144 0.20938 0.2167 0.25123 0.268 RANDOM 41.182
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 -0.16 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.316 r_dihedral_angle_4_deg 16.486 r_dihedral_angle_3_deg 14.372 r_dihedral_angle_1_deg 6.462 r_scangle_it 2.779 r_scbond_it 1.695 r_angle_refined_deg 1.382 r_mcangle_it 0.998 r_angle_other_deg 0.884 r_mcbond_it 0.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.316 r_dihedral_angle_4_deg 16.486 r_dihedral_angle_3_deg 14.372 r_dihedral_angle_1_deg 6.462 r_scangle_it 2.779 r_scbond_it 1.695 r_angle_refined_deg 1.382 r_mcangle_it 0.998 r_angle_other_deg 0.884 r_mcbond_it 0.551 r_mcbond_other 0.132 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1316 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 6
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling