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Recombinant peptide: N-glycanase F (PNGase F)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PGS PDB ENTRY 1PGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 295.15 25% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K
Crystal Properties Matthews coefficient Solvent content 2.31 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.96 α = 90 b = 90.56 β = 112.3 c = 48.81 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 120 IMAGE PLATE RIGAKU RAXIS IV++ 2009-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.542
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 1.57 40.41 96.6 0.057 43449 41972
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PGS 1.57 34.02 41972 2256 100 0.1524 0.151 0.1778 0.1921 RANDOM 18.3064
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] 1.11 -0.4 -0.92 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.01 r_dihedral_angle_3_deg 13.677 r_dihedral_angle_4_deg 10.833 r_dihedral_angle_1_deg 7.08 r_scangle_it 5.044 r_scbond_it 3.282 r_mcangle_it 2.475 r_angle_refined_deg 1.821 r_mcbond_it 1.608 r_angle_other_deg 0.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.01 r_dihedral_angle_3_deg 13.677 r_dihedral_angle_4_deg 10.833 r_dihedral_angle_1_deg 7.08 r_scangle_it 5.044 r_scbond_it 3.282 r_mcangle_it 2.475 r_angle_refined_deg 1.821 r_mcbond_it 1.608 r_angle_other_deg 0.927 r_mcbond_other 0.535 r_chiral_restr 0.122 r_bond_refined_d 0.02 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2452 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 78
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection XSCALE data scaling