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The structure of the catalytic domain of NcLPMO9C from the filamentous fungus Neurospora crassa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EIR PDB ENTRY 4EIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.1 0.2M AMMONIUM CITRATE, 20% PEG 3350, PH 5.1
Crystal Properties Matthews coefficient Solvent content 1.99 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.258 α = 90 b = 66.755 β = 101.26 c = 66.077 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 MARMOSAIC 225 mm CCD MIRRORS 2014-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 MAX II I911-3
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 1.56 64.81 91.3 0.04 15.5 3.3 49150 2 12.6
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 1.56 1.59 29.2 3.1 1.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4EIR 1.56 64.805 48932 2423 91.057 0.158 0.1563 0.1683 0.1876 0.1957 RANDOM 13.496
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] -1.209 -0.206 2.347 -0.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.98 r_dihedral_angle_3_deg 10.489 r_dihedral_angle_4_deg 9.067 r_dihedral_angle_1_deg 6.231 r_angle_refined_deg 1.158 r_mcangle_it 1.108 r_scangle_it 1.006 r_angle_other_deg 0.718 r_mcbond_it 0.616 r_mcbond_other 0.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.98 r_dihedral_angle_3_deg 10.489 r_dihedral_angle_4_deg 9.067 r_dihedral_angle_1_deg 6.231 r_angle_refined_deg 1.158 r_mcangle_it 1.108 r_scangle_it 1.006 r_angle_other_deg 0.718 r_mcbond_it 0.616 r_mcbond_other 0.616 r_scbond_it 0.607 r_nbd_refined 0.224 r_nbtor_refined 0.169 r_nbd_other 0.155 r_xyhbond_nbd_refined 0.093 r_chiral_restr 0.069 r_metal_ion_refined 0.05 r_xyhbond_nbd_other 0.049 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_other 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_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 3280 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing