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Crystal structure of class C beta-lactamase Mox-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 20% PEG8000, 0.2M zinc acetate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.22 44.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.617 α = 90 b = 59.378 β = 102.19 c = 62.685 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 100 CCD ADSC QUANTUM 270 2012-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 1.38 61.273 98.96 73169 72411
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.398 86.48
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ZKJ 1.5 25 57086 53733 2874 99.16 0.16485 0.1636 0.18913 0.204 RANDOM 22.151
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] 0.16 1 -1.26 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.974 r_dihedral_angle_4_deg 13.357 r_sphericity_free 12.74 r_dihedral_angle_3_deg 10.508 r_rigid_bond_restr 10.045 r_sphericity_bonded 6.094 r_dihedral_angle_1_deg 6.058 r_scbond_it 1.7 r_mcangle_it 1.607 r_angle_refined_deg 1.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.974 r_dihedral_angle_4_deg 13.357 r_sphericity_free 12.74 r_dihedral_angle_3_deg 10.508 r_rigid_bond_restr 10.045 r_sphericity_bonded 6.094 r_dihedral_angle_1_deg 6.058 r_scbond_it 1.7 r_mcangle_it 1.607 r_angle_refined_deg 1.321 r_mcbond_it 1.053 r_mcbond_other 1.036 r_angle_other_deg 0.774 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2620 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection