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Crystal structure of the Class A beta-lactamase L2 from Stenotrophomonas maltophilia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BZA PDB ENTRY 1BZA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 ammonium sulfate 1.5M, sodium cacodylate 0.1M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.55 65.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.503 α = 90 b = 135.503 β = 90 c = 94.856 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 283 IMAGE PLATE MARRESEARCH 2001-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LURE BEAMLINE DW32 0.9485 LURE DW32
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 1.85 30 99.2 0.064 22.7 6.1 75048 2.5 25.4
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) 1.85 1.95 95.2 0.286 2.6 5.5 10357
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 (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 1BZA 1.85 30 70264 4719 99.1 0.164 0.155 0.147 0.1503 0.164 0.1679 RANDOM 17.3
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.057 r_dihedral_angle_1_deg 4.497 r_scangle_it 4.399 r_mcangle_it 3.092 r_scbond_it 2.804 r_mcbond_it 1.926 r_angle_refined_deg 1.753 r_nbd_refined 0.25 r_chiral_restr 0.144 r_xyhbond_nbd_refined 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.057 r_dihedral_angle_1_deg 4.497 r_scangle_it 4.399 r_mcangle_it 3.092 r_scbond_it 2.804 r_mcbond_it 1.926 r_angle_refined_deg 1.753 r_nbd_refined 0.25 r_chiral_restr 0.144 r_xyhbond_nbd_refined 0.142 r_symmetry_vdw_refined 0.14 r_symmetry_hbond_refined 0.082 r_bond_refined_d 0.022 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4049 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 20
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling