☰ Navigation Tabs
Structure of CYP107L2 from Streptomyces avermitilis with lauric acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 287 Lithium sulfate monohydrate, Tris-HCL, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.79 55.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.08 α = 90 b = 118.371 β = 105.51 c = 66.039 γ = 90
Symmetry Space Group P 1 21 1
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 270 2013-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97952 PAL/PLS 5C (4A)
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 2.39 50 99.4 25.5 4 37158
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 2.39 2.44 95.8 0.447 3.9 3.9
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 2CD8 2.39 47.43 35267 1862 98.8 0.22961 0.22586 0.2294 0.30085 0.3018 RANDOM 44.737
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] -0.03 0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.199 r_dihedral_angle_3_deg 18.08 r_dihedral_angle_4_deg 17.934 r_dihedral_angle_1_deg 7.553 r_long_range_B_refined 7.256 r_long_range_B_other 7.255 r_mcangle_it 4.703 r_mcangle_other 4.703 r_scangle_other 4.619 r_mcbond_it 3.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.199 r_dihedral_angle_3_deg 18.08 r_dihedral_angle_4_deg 17.934 r_dihedral_angle_1_deg 7.553 r_long_range_B_refined 7.256 r_long_range_B_other 7.255 r_mcangle_it 4.703 r_mcangle_other 4.703 r_scangle_other 4.619 r_mcbond_it 3.037 r_mcbond_other 3.036 r_scbond_it 2.967 r_scbond_other 2.964 r_angle_refined_deg 1.727 r_angle_other_deg 1.071 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6072 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement DENZO data processing MOLREP model building PHASER phasing HKL-2000 data processing Coot model building