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Crystal Structure analysis of a Dehalogenase with intermediate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 20% PEG 4000, 0.65M Ammonium Sulphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.01 69.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.743 α = 90 b = 103.743 β = 90 c = 134.794 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2004-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.6 29.24 99.9 0.133 10.13 3.49 26826 26322 1 55.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.67 99.9 1.41 3.11 1919
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 FOURIER SYNTHESIS THROUGHOUT 2NO4 2.6 29.24 25671 1315 99.87 0.199 0.196 0.1965 0.252 0.1932 RANDOM 40.139
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.664 r_dihedral_angle_3_deg 20.261 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_1_deg 7.057 r_mcangle_it 3.011 r_scangle_it 2.741 r_mcbond_it 1.859 r_angle_refined_deg 1.845 r_scbond_it 1.817 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.664 r_dihedral_angle_3_deg 20.261 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_1_deg 7.057 r_mcangle_it 3.011 r_scangle_it 2.741 r_mcbond_it 1.859 r_angle_refined_deg 1.845 r_scbond_it 1.817 r_nbtor_refined 0.322 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.243 r_symmetry_vdw_refined 0.221 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.124 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3592 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 84
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection MOSFLM data reduction REFMAC phasing