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Phospholyase A1RDF1 from Arthrobacter in complex with phosphoethanolamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G4I PDB ENTRY 5G4I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 24% (W/V) PEG 3350, 0.2 M (NH4)2SO4 AND 3% (V/V) 2-METHYL-2,4-PENTANEDIOL IN 0.1 M BIS-TRIS PROPANE BUFFER AT PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.33 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.166 α = 90 b = 96.371 β = 90 c = 121.897 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 120 PIXEL DECTRIS PILATUS 6M 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.87 64.59 99.8 0.08 14.5 6.5 74689 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) 1 1.87 1.95 99.9 0.67 2.6 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5G4I 1.87 75.6 70978 3636 99.77 0.16884 0.16731 0.19943 0.1968 RANDOM 25.913
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] -1.84 0.51 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.885 r_dihedral_angle_4_deg 18.596 r_dihedral_angle_3_deg 14.118 r_dihedral_angle_1_deg 6.287 r_scbond_it 3.127 r_mcangle_it 3.081 r_mcbond_it 2.382 r_mcbond_other 2.381 r_angle_refined_deg 1.915 r_angle_other_deg 1.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.885 r_dihedral_angle_4_deg 18.596 r_dihedral_angle_3_deg 14.118 r_dihedral_angle_1_deg 6.287 r_scbond_it 3.127 r_mcangle_it 3.081 r_mcbond_it 2.382 r_mcbond_other 2.381 r_angle_refined_deg 1.915 r_angle_other_deg 1.478 r_chiral_restr 0.227 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.008 r_gen_planes_other 0.006 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_mcangle_other r_scbond_other r_scangle_it 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 6300 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing