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Strictosidine Synthase from Ophiorrhiza pumila in complex with (S)-1-isobutyl-2,3,4,9-tetrahydro-1H-beta-carboline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1 M Tris-HCl pH 8.0; 0.3 M NH4Cl; 20% PEG 6K
Crystal Properties Matthews coefficient Solvent content 2.49 50.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.085 α = 90 b = 78.435 β = 92.47 c = 61.84 γ = 90
Symmetry Space Group C 1 2 1
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-F 2016-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.01 41.58 99.2 0.05 0.04 1 7.8 4 24041
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.04 0.61 0.51 0.9 2.1
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 2FP9 2.01 41.58 22890 1141 99.12 0.2148 0.2122 0.217 0.2685 0.2686 RANDOM 54.995
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] 6.75 -7 -3.75 -2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.42 r_dihedral_angle_4_deg 21.149 r_dihedral_angle_3_deg 17.528 r_dihedral_angle_1_deg 8.643 r_angle_refined_deg 1.533 r_angle_other_deg 1.257 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.42 r_dihedral_angle_4_deg 21.149 r_dihedral_angle_3_deg 17.528 r_dihedral_angle_1_deg 8.643 r_angle_refined_deg 1.533 r_angle_other_deg 1.257 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2327 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing