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Crystal structure of the H253D mutant of McoG from Aspergillus niger
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LM8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 296 20% PEG 3350, 0.2 M NaCl, 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.61 52.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.273 α = 90 b = 60.498 β = 94.96 c = 53.744 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 100 PIXEL DECTRIS PILATUS 6M 2013-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.951 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.49 29.24 98.1 0.074 0.997 9.09 3.2 101840 -3 27.251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.58 91.6 0.987 0.574 0.97
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 FOURIER SYNTHESIS THROUGHOUT 5LM8 1.49 30 96750 5081 98.15 0.17276 0.17153 0.1794 0.19572 0.2002 RANDOM 33.548
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] -1.73 0.35 1.85 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.354 r_dihedral_angle_4_deg 13.526 r_dihedral_angle_3_deg 11.108 r_dihedral_angle_1_deg 6.975 r_long_range_B_refined 5.993 r_scbond_it 2.121 r_mcangle_it 2.113 r_mcbond_it 1.503 r_angle_refined_deg 1.307 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.354 r_dihedral_angle_4_deg 13.526 r_dihedral_angle_3_deg 11.108 r_dihedral_angle_1_deg 6.975 r_long_range_B_refined 5.993 r_scbond_it 2.121 r_mcangle_it 2.113 r_mcbond_it 1.503 r_angle_refined_deg 1.307 r_chiral_restr 0.093 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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_it r_scangle_other 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 4374 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing