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X-ray analysis of lysozyme in the presence of 200 mM Arg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A34 PDB ENTRY 3A34
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 293 0.05M Sodium Acetate, 1.6M Sodium Chloride, 0.2M Arg, pH 4.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.299 α = 90 b = 78.299 β = 90 c = 37.284 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 CCD RIGAKU JUPITER 210 mirrors 2009-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.000 SPring-8 BL32B2
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 1.49 50 99.8 0.034 15.2 18454
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.49 1.54 97.7 0.13 19.1 13.9 3548
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 PDB ENTRY 3A34 1.49 39.15 18454 996 99.98 0.1762 0.1747 0.1748 0.20459 0.2032 RANDOM 13.27
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] -0.18 -0.18 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.435 r_dihedral_angle_4_deg 14.585 r_dihedral_angle_3_deg 11.48 r_dihedral_angle_1_deg 5.752 r_scangle_it 3.86 r_scbond_it 2.679 r_mcangle_it 1.673 r_angle_refined_deg 1.593 r_mcbond_it 0.986 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.435 r_dihedral_angle_4_deg 14.585 r_dihedral_angle_3_deg 11.48 r_dihedral_angle_1_deg 5.752 r_scangle_it 3.86 r_scbond_it 2.679 r_mcangle_it 1.673 r_angle_refined_deg 1.593 r_mcbond_it 0.986 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.24 r_symmetry_hbond_refined 0.237 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.108 r_metal_ion_refined 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 9
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling