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E. coli (lacZ) beta-galactosidase (E416Q)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DP0 PDB entry 1DP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 PEG8000, NaCl, MgCl2, DTT, Bis-Tris, pH6.5, HANGING DROP AT 288K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.66 53.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.23 α = 90 b = 162.34 β = 90 c = 202.06 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 210 KOHZU: Double Crystal SI(111) 2008-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11589 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2 58.42 87 0.149 0.198 5.2 3.29 395192 120198 37.5
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) 2.7 2.85 90.2 0.408 0.539 2.5 3.22 58195
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1DP0 2 53.38 291901 120198 4186 100 0.18143 0.18141 0.18085 0.1809 0.22042 0.2209 RANDOM 24.347
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.823 r_dihedral_angle_4_deg 14.535 r_dihedral_angle_3_deg 12.425 r_dihedral_angle_1_deg 5.694 r_scangle_it 3.084 r_scbond_it 1.993 r_mcangle_it 1.585 r_angle_refined_deg 0.971 r_mcbond_it 0.903 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.823 r_dihedral_angle_4_deg 14.535 r_dihedral_angle_3_deg 12.425 r_dihedral_angle_1_deg 5.694 r_scangle_it 3.084 r_scbond_it 1.993 r_mcangle_it 1.585 r_angle_refined_deg 0.971 r_mcbond_it 0.903 r_nbtor_refined 0.299 r_nbd_refined 0.166 r_metal_ion_refined 0.13 r_symmetry_vdw_refined 0.123 r_symmetry_hbond_refined 0.105 r_xyhbond_nbd_refined 0.093 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 32500 Nucleic Acid Atoms Solvent Atoms 3832 Heterogen Atoms 580
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection MOSFLM data reduction SCALA data scaling CNS phasing