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High resolution X-ray analysis of Arg-lysozyme complex in the presence of 500 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 0.05 M Sodium Acetate
1.6 M Sodium Chloride
0.5 M Arg, pH 4.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.033 α = 90 b = 78.033 β = 90 c = 37.752 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 ADSC QUANTUM 210 mirrors 2010-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
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 50 0.052 14.7 34994
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) 1.2 1.24 100 0.46 4.3 14.4 6969
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 1.2 39.02 34994 1839 99.53 0.13866 0.13718 0.1368 0.16664 0.1675 RANDOM 14.183
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] 0.09 0.09 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.073 r_dihedral_angle_4_deg 17.485 r_dihedral_angle_3_deg 12.597 r_sphericity_free 11.03 r_sphericity_bonded 6.301 r_dihedral_angle_1_deg 6.044 r_scangle_it 5.058 r_scbond_it 3.69 r_mcangle_it 2.672 r_rigid_bond_restr 2.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.073 r_dihedral_angle_4_deg 17.485 r_dihedral_angle_3_deg 12.597 r_sphericity_free 11.03 r_sphericity_bonded 6.301 r_dihedral_angle_1_deg 6.044 r_scangle_it 5.058 r_scbond_it 3.69 r_mcangle_it 2.672 r_rigid_bond_restr 2.136 r_mcbond_it 1.862 r_angle_refined_deg 1.79 r_symmetry_hbond_refined 0.314 r_nbtor_refined 0.306 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.147 r_metal_ion_refined 0.034 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 49
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling