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Crystal structure of fluorophore-labeled 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 7.5 291 PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.23 44.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.386 α = 90 b = 91.626 β = 104.5 c = 66.008 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 2008-07-15 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) 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 1.9 45.8 39490
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 1.9 40 37382 1983 99.87 0.2 0.19747 0.2065 0.24634 0.2488 RANDOM 22.694
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] -0.03 -0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 18.559 r_dihedral_angle_3_deg 16.153 r_dihedral_angle_1_deg 6.25 r_scangle_it 3.377 r_scbond_it 2.074 r_angle_refined_deg 1.615 r_mcangle_it 1.497 r_mcbond_it 0.892 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 18.559 r_dihedral_angle_3_deg 16.153 r_dihedral_angle_1_deg 6.25 r_scangle_it 3.377 r_scbond_it 2.074 r_angle_refined_deg 1.615 r_mcangle_it 1.497 r_mcbond_it 0.892 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.282 r_nbd_refined 0.252 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.152 r_chiral_restr 0.124 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 3983 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement