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Crystal Structure of fluorescein-labeled Class A -beta lactamase PenP in complex with cefotaxime
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.27 45.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.538 α = 90 b = 91.524 β = 104.22 c = 66.302 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2007-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.4 46 0.148 18395
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 MOLECULAR REPLACEMENT THROUGHOUT 4BLM 3.5 40.23 5798 308 94.92 0.17952 0.1763 0.1808 0.2359 0.2137 RANDOM 13.684
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] -1.97 -1.38 4.27 -2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.384 r_dihedral_angle_3_deg 24.733 r_dihedral_angle_4_deg 23.554 r_dihedral_angle_1_deg 11.388 r_scangle_it 4.06 r_angle_refined_deg 3.999 r_scbond_it 2.666 r_mcangle_it 1.426 r_mcbond_it 1.061 r_nbtor_refined 0.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.384 r_dihedral_angle_3_deg 24.733 r_dihedral_angle_4_deg 23.554 r_dihedral_angle_1_deg 11.388 r_scangle_it 4.06 r_angle_refined_deg 3.999 r_scbond_it 2.666 r_mcangle_it 1.426 r_mcbond_it 1.061 r_nbtor_refined 0.355 r_nbd_refined 0.346 r_symmetry_vdw_refined 0.25 r_chiral_restr 0.243 r_symmetry_hbond_refined 0.239 r_xyhbond_nbd_refined 0.236 r_bond_refined_d 0.051 r_gen_planes_refined 0.021 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_refined 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 3873 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 52
Software Software Software Name Purpose CrystalClear data collection REFMAC refinement CrystalClear data reduction CrystalClear data scaling