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Beta-galactosidase (E. coli) in the presence of potassium chloride.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 100 mM Bis-Tris
100 mM NaCl
200 mM MgCl2
9-12 % PEG 8000
Microseeded
Serial soaked in buffer with 100 mM KCl, yielding 100 mM KCl and 16 nM NaCl
Cryoprotected by serial soaks over several hours in 5% increments to 30%/70% (v/v) DMSO/above KCl buffer
Cooled in the nitrogen stream at 100 K
Crystal Properties Matthews coefficient Solvent content 2.7 54.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.29 α = 90 b = 168.1 β = 90 c = 200.31 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 4 1998-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.979 ALS 5.0.2
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 1.6 56.5 92.9 0.075 9.5 2.9 604015
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 1.6 1.69 87.5 0.232 3.7 2.6
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 1DP0 1.6 55.81 595237 8778 92.06 0.1602 0.15979 0.188 0.1929 RANDOM 16.155
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 0.27 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.342 r_dihedral_angle_4_deg 15.973 r_dihedral_angle_3_deg 12.916 r_sphericity_bonded 11.598 r_dihedral_angle_1_deg 6.819 r_angle_refined_deg 1.963 r_chiral_restr 0.153 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.342 r_dihedral_angle_4_deg 15.973 r_dihedral_angle_3_deg 12.916 r_sphericity_bonded 11.598 r_dihedral_angle_1_deg 6.819 r_angle_refined_deg 1.963 r_chiral_restr 0.153 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32632 Nucleic Acid Atoms Solvent Atoms 4451 Heterogen Atoms 559
Software Software Software Name Purpose REFMAC refinement