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The mutant variant of PNGM-1, H93 was substituuted 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 7.1 287 50 mM HEPES pH 7.1, 10% PEG 4000, 150 mM Magnesium acetate, 200 mM Ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.755 α = 90 b = 82.792 β = 111.1 c = 164.047 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) 1.00003 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.61 50 99.1 0.086 0.093 0.036 8.6 6.4 388155
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 1.61 1.64 97.5 0.31 0.339 0.135 0.96 6
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 1.61 41.51 368596 19534 98.95 0.1977 0.1963 0.2051 0.2227 0.2308 RANDOM 13.337
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.923 r_dihedral_angle_4_deg 16.451 r_dihedral_angle_3_deg 14.959 r_dihedral_angle_1_deg 7.683 r_angle_refined_deg 1.807 r_angle_other_deg 1.519 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.923 r_dihedral_angle_4_deg 16.451 r_dihedral_angle_3_deg 14.959 r_dihedral_angle_1_deg 7.683 r_angle_refined_deg 1.807 r_angle_other_deg 1.519 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23424 Nucleic Acid Atoms Solvent Atoms 1110 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction HKL-3000 phasing