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AmpC beta-lactamase with bound Phthalamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HPU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 291 1.7M KiPO4, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.54 51.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.683 α = 90 b = 77.255 β = 116.53 c = 97.939 γ = 90
Symmetry Space Group C 1 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 CCD ADSC QUANTUM 315 2007-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
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 1.8 50 99.4 0.053 14.2 2.9 72824
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 1.8 1.86 98.3 0.356 2.9 7167
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 THROUGHOUT 2hpu 1.8 30 72804 3674 99.41 0.164 0.163 0.1688 0.193 0.1955 RANDOM 17.405
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] 0.61 0.62 -0.44 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.837 r_dihedral_angle_4_deg 15.785 r_dihedral_angle_3_deg 12.797 r_dihedral_angle_1_deg 9.359 r_scangle_it 2.837 r_scbond_it 2.218 r_angle_refined_deg 1.369 r_mcbond_it 1.3 r_mcangle_it 1.183 r_angle_other_deg 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.837 r_dihedral_angle_4_deg 15.785 r_dihedral_angle_3_deg 12.797 r_dihedral_angle_1_deg 9.359 r_scangle_it 2.837 r_scbond_it 2.218 r_angle_refined_deg 1.369 r_mcbond_it 1.3 r_mcangle_it 1.183 r_angle_other_deg 0.95 r_symmetry_hbond_refined 0.362 r_symmetry_vdw_other 0.261 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.209 r_nbd_other 0.188 r_nbtor_refined 0.179 r_mcbond_other 0.166 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.117 r_nbtor_other 0.087 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5600 Nucleic Acid Atoms Solvent Atoms 608 Heterogen Atoms 108
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection REFMAC phasing