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Bacillus cereus Zn-dependent metallo-beta-lactamase at pH 7 - new refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 20% PEG3350, 180mM K2SO4, protein at 15mg/ml in 10mM Tris-HCl pH7, 50mM NaCl, 1mM DTT, 1mM Zn2SO4, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 46.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.603 α = 90 b = 60.419 β = 93.28 c = 69.513 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2013-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.25 35.4 87.4 9273
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 2.25 2.308 80.11
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 4NQ4 2.25 35.4 8356 915 87.43 0.1588 0.1525 0.1618 0.2187 0.2239 RANDOM 38.215
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] -0.61 -0.3 3.36 -2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.287 r_sphericity_bonded 22.646 r_dihedral_angle_3_deg 13.707 r_dihedral_angle_4_deg 13.55 r_dihedral_angle_1_deg 7.396 r_angle_refined_deg 1.572 r_angle_other_deg 0.949 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.287 r_sphericity_bonded 22.646 r_dihedral_angle_3_deg 13.707 r_dihedral_angle_4_deg 13.55 r_dihedral_angle_1_deg 7.396 r_angle_refined_deg 1.572 r_angle_other_deg 0.949 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1668 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 8
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction