☰ Navigation Tabs
The mutant variant of PNGM-1. H91 was substituted for alanine to study metal coordination.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J4N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5.4 287 0.1 M Sodium acetate, 1.5 M Sodium formate, 0.08 M CaCl2 and 10% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.38 α = 90 b = 83.057 β = 110.69 c = 163.581 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 315r 2013-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97940 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.94 50 96.6 0.122 0.122 0.134 0.055 0.989 5.1 5.1 211626
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 1.99 95.6 0.397 0.452 0.209 0.716 4.1
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 6j4n 1.94 49.04 204033 10778 95.13 0.2121 0.2099 0.2161 0.2546 0.2567 RANDOM 26.224
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] -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.823 r_dihedral_angle_4_deg 20.097 r_dihedral_angle_3_deg 16.315 r_dihedral_angle_1_deg 7.978 r_angle_refined_deg 1.488 r_angle_other_deg 1.291 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.823 r_dihedral_angle_4_deg 20.097 r_dihedral_angle_3_deg 16.315 r_dihedral_angle_1_deg 7.978 r_angle_refined_deg 1.488 r_angle_other_deg 1.291 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22738 Nucleic Acid Atoms Solvent Atoms 1881 Heterogen Atoms 8
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction HKL-3000 phasing