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In situ lysozyme crystallized on a MiTeGen micromesh with benzamidine ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LYZ PDB ENTRY 1LYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 In situ crystallization on micromesh 4.6 290 4% sodium chloride, 100mM sodium acetate pH 4.6, 120mg/ml, In situ crystallization on micromesh, temperature 290K
Crystal Properties Matthews coefficient Solvent content 1.98 37.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.15 α = 90 b = 79.15 β = 90 c = 36.28 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-10-13 M SINGLE WAVELENGTH 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.1 NSLS X12C 2 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A 3 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 1.2 26.76 97.78 0.079 30.46 1.9 34775 34003 2 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 97.78 0.079 0.079 30.46 1.9 34003
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1LYZ 1.2 26.76 2 34775 34003 1795 97.78 0.23007 0.23007 0.22902 0.25073 0.2685 RANDOM 19.173
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] -1.2 -1.2 2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.641 r_dihedral_angle_4_deg 17.865 r_dihedral_angle_3_deg 14.319 r_dihedral_angle_1_deg 7.231 r_long_range_B_refined 6.524 r_long_range_B_other 5.964 r_scangle_other 3.811 r_scbond_it 2.63 r_scbond_other 2.628 r_angle_refined_deg 2.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.641 r_dihedral_angle_4_deg 17.865 r_dihedral_angle_3_deg 14.319 r_dihedral_angle_1_deg 7.231 r_long_range_B_refined 6.524 r_long_range_B_other 5.964 r_scangle_other 3.811 r_scbond_it 2.63 r_scbond_other 2.628 r_angle_refined_deg 2.441 r_mcangle_other 1.976 r_mcangle_it 1.96 r_mcbond_it 1.57 r_mcbond_other 1.51 r_angle_other_deg 1.131 r_chiral_restr 0.168 r_bond_refined_d 0.029 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 1001 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 24
Software Software Software Name Purpose CBASS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling