☰ Navigation Tabs
Zinc-beta-lactamase l1 from stenotrophomonas maltophilia (apo form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SML PDB ENTRY 1SML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 280 AS, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.05 α = 90 b = 105.05 β = 90 c = 196.53 γ = 120
Symmetry Space Group P 62 2 2
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 MARRESEARCH 2005-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.05 20 99.1 0.097 0.097 7.4 7 40479 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.103 99.1 0.49 0.49 1.9 7.1
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 1SML 2.05 19.89 38425 2023 98.9 0.1631 0.16286 0.16038 0.1729 0.20937 0.1743 RANDOM 18.596
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] 0.05 0.02 0.05 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.823 r_dihedral_angle_3_deg 13.773 r_dihedral_angle_4_deg 13.567 r_dihedral_angle_1_deg 6.427 r_scangle_it 3.494 r_scbond_it 2.473 r_angle_refined_deg 1.621 r_mcangle_it 1.402 r_mcbond_it 1.205 r_angle_other_deg 0.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.823 r_dihedral_angle_3_deg 13.773 r_dihedral_angle_4_deg 13.567 r_dihedral_angle_1_deg 6.427 r_scangle_it 3.494 r_scbond_it 2.473 r_angle_refined_deg 1.621 r_mcangle_it 1.402 r_mcbond_it 1.205 r_angle_other_deg 0.866 r_nbd_refined 0.341 r_symmetry_vdw_other 0.243 r_mcbond_other 0.233 r_nbd_other 0.201 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.151 r_symmetry_vdw_refined 0.147 r_chiral_restr 0.096 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4002 Nucleic Acid Atoms Solvent Atoms 526 Heterogen Atoms 58
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CCP4 model building REFMAC refinement CCP4 data scaling CCP4 phasing