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The mutant variant of PNGM-1. H279A 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 4.63 73.45
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) 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 1.94 50 96.6 0.122 0.134 0.055 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 1.96 49.04 204033 10778 95.13 0.5205 0.5186 0.5201 0.5568 0.5583 RANDOM 20.693
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 34.718 r_dihedral_angle_4_deg 19.314 r_dihedral_angle_3_deg 16.775 r_dihedral_angle_1_deg 8.484 r_angle_refined_deg 1.447 r_angle_other_deg 1.128 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.718 r_dihedral_angle_4_deg 19.314 r_dihedral_angle_3_deg 16.775 r_dihedral_angle_1_deg 8.484 r_angle_refined_deg 1.447 r_angle_other_deg 1.128 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11344 Nucleic Acid Atoms Solvent Atoms 566 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction HKL-3000 phasing