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Apo form of C-type lysozyme from the upper gastrointestinal tract of Opisthocomus hoatzin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 150 nl of protein was mixed with 150 nl of mother liquor solution. Crystals grew in 0.1 M MIB system (malonic acid, imidazole, boric acid) pH 4.0 and 25% Peg 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.973 α = 90 b = 54.895 β = 90 c = 65.319 γ = 90
Symmetry Space Group P 21 21 21
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 315 2009-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.5 42.06 99.8 0.074 0.998 12.3 5 21950
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 1.5 1.53 0.535 0.646 1.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1gft 1.5 42.06 21899 1108 99.727 0.118 0.1156 0.1155 0.1657 0.1663 15.187
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] -0.046 -0.08 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.751 r_rigid_bond_restr 12.56 r_dihedral_angle_3_deg 11.733 r_dihedral_angle_4_deg 8.24 r_dihedral_angle_1_deg 6.717 r_lrange_it 4.591 r_lrange_other 4.589 r_scangle_it 3.178 r_scangle_other 3.176 r_scbond_it 2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.751 r_rigid_bond_restr 12.56 r_dihedral_angle_3_deg 11.733 r_dihedral_angle_4_deg 8.24 r_dihedral_angle_1_deg 6.717 r_lrange_it 4.591 r_lrange_other 4.589 r_scangle_it 3.178 r_scangle_other 3.176 r_scbond_it 2.7 r_scbond_other 2.697 r_angle_other_deg 2.429 r_mcangle_other 2.225 r_mcangle_it 2.203 r_mcbond_it 1.802 r_mcbond_other 1.772 r_angle_refined_deg 1.744 r_symmetry_xyhbond_nbd_refined 0.277 r_symmetry_nbd_refined 0.266 r_nbd_refined 0.239 r_symmetry_nbd_other 0.223 r_xyhbond_nbd_refined 0.211 r_nbd_other 0.185 r_nbtor_refined 0.18 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.076 r_bond_other_d 0.037 r_bond_refined_d 0.015 r_gen_planes_other 0.013 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1000 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing