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Crystal Structure of DapA (PA1010) at 1.6 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OJP PDB entry 2OJP chain-A edited
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293 0.1 M Tris-HCl pH 7.6, 0.2 M MgCl2, 18% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.11 α = 95.7 b = 51.74 β = 90.02 c = 140.35 γ = 113.27
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r channel cut ESRF monochromator and a new torodial focusing mirror 2010-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97700 ESRF ID14-4
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 1.59 41.25 92.7 0.053 0.053 9.5 2 139082 139082 3.1 3.1 15.7
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) 1 1.59 1.67 92.2 0.281 0.281 3.1 2 20245
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2OJP chain-A edited 1.59 40 3.1 132070 132070 7011 92.66 0.14948 0.14948 0.14683 0.158 0.1992 0.2049 RANDOM 13.103
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 -0.14 0.53 0.37 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.157 r_dihedral_angle_4_deg 19.579 r_dihedral_angle_3_deg 13.447 r_sphericity_free 9.676 r_dihedral_angle_1_deg 5.979 r_scangle_it 5.803 r_scbond_it 4.041 r_sphericity_bonded 3.517 r_mcangle_it 2.685 r_rigid_bond_restr 2.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.157 r_dihedral_angle_4_deg 19.579 r_dihedral_angle_3_deg 13.447 r_sphericity_free 9.676 r_dihedral_angle_1_deg 5.979 r_scangle_it 5.803 r_scbond_it 4.041 r_sphericity_bonded 3.517 r_mcangle_it 2.685 r_rigid_bond_restr 2.119 r_angle_refined_deg 2.023 r_mcbond_it 1.931 r_angle_other_deg 1.13 r_mcbond_other 0.924 r_chiral_restr 0.133 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8768 Nucleic Acid Atoms Solvent Atoms 875 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling