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Crystal structure of polyneuridine aldehyde esterase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XKL PDB ENTRY 1XKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 0.20M BIS-TRIS, 0.25M LI2SO4, 25%POLYETHYLENE GLYCOL 3350, PH6.30., pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.64 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.758 α = 90 b = 176.917 β = 90 c = 75.697 γ = 90
Symmetry Space Group C 2 2 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 CCD MARRESEARCH DOUBLE CRYSTAL SI 111 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.1 20 100 0.07 32.5 9.6 36861 -3 38.42
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 2.1 2.14 100 0.54 4.4 9.3
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 PDB ENTRY 1XKL 2.1 20 35684 1046 100 0.183 0.182 0.3846 0.231 0.4226 RANDOM 39.17
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] 3.17 -1.32 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.099 r_dihedral_angle_4_deg 20.104 r_dihedral_angle_3_deg 15.995 r_dihedral_angle_1_deg 7.55 r_scangle_it 5.229 r_scbond_it 3.63 r_angle_refined_deg 1.897 r_mcangle_it 1.626 r_mcbond_it 0.899 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.099 r_dihedral_angle_4_deg 20.104 r_dihedral_angle_3_deg 15.995 r_dihedral_angle_1_deg 7.55 r_scangle_it 5.229 r_scbond_it 3.63 r_angle_refined_deg 1.897 r_mcangle_it 1.626 r_mcbond_it 0.899 r_chiral_restr 0.122 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 4034 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling Auto-Rickshaw phasing MOLREP phasing REFMAC refinement