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Crystal structure of beta-lactamase OXY-1-1 from Klebsiella oxytoca
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 4.5 296 25%(w/v) PEG 4000, 0.1M sodium acetate buffer, 0.2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.545 α = 90 b = 73.431 β = 90 c = 84.561 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2000-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.0292 MAX II I711
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 1.93 56 96.9 0.052 14.8 4.6 21787 28.8
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 1.93 2 96.1 0.129 4.2 2091
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BZA 1.93 55.47 22433 21754 1120 96.97 0.211 0.184 0.182 0.225 0.2885 RANDOM 15.24
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] 0.59 0.04 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.582 r_dihedral_angle_3_deg 11.751 r_dihedral_angle_4_deg 11.324 r_dihedral_angle_1_deg 5.487 r_scangle_it 2.514 r_scbond_it 1.717 r_angle_refined_deg 1.236 r_mcangle_it 0.923 r_mcbond_it 0.627 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.582 r_dihedral_angle_3_deg 11.751 r_dihedral_angle_4_deg 11.324 r_dihedral_angle_1_deg 5.487 r_scangle_it 2.514 r_scbond_it 1.717 r_angle_refined_deg 1.236 r_mcangle_it 0.923 r_mcbond_it 0.627 r_nbtor_refined 0.293 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.151 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1941 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data scaling CNS phasing