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Crystal Structure of fluorescein-labeled Class A -lactamase PenP
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 2.25 45.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.354 α = 90 b = 92.34 β = 104.84 c = 66.415 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 1.8 46 0.084 45125
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 1.8 31.59 42614 2274 95.9 0.21221 0.20901 0.21 0.27278 0.2753 RANDOM 22.31
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] -0.02 0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.042 r_dihedral_angle_4_deg 19.636 r_dihedral_angle_3_deg 18.757 r_dihedral_angle_1_deg 9.405 r_scangle_it 4.111 r_scbond_it 2.761 r_angle_refined_deg 2.22 r_mcangle_it 1.731 r_mcbond_it 1.077 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.042 r_dihedral_angle_4_deg 19.636 r_dihedral_angle_3_deg 18.757 r_dihedral_angle_1_deg 9.405 r_scangle_it 4.111 r_scbond_it 2.761 r_angle_refined_deg 2.22 r_mcangle_it 1.731 r_mcbond_it 1.077 r_nbtor_refined 0.305 r_nbd_refined 0.272 r_symmetry_vdw_refined 0.212 r_chiral_restr 0.192 r_xyhbond_nbd_refined 0.184 r_symmetry_hbond_refined 0.177 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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 4007 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 42
Software Software Software Name Purpose CrystalClear data collection REFMAC refinement CrystalClear data reduction CrystalClear data scaling