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Crystal structure of an amidohydrolase (COG3618) from burkholderia multivorans (TARGET EFI-500235) with bound ZN, space group P3221
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DNM PDB ENTRY 4DNM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop vapor diffuction 7.5 298 Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 0.5 mM ZnCl, 0.5 mM D-arabonate-1,4-lactone; Reservoir (20% Peg3350, 100 mM HEPES pH 7.5); Cryoprotection (Reservoir, 5 mM Zn, 25 mM D-arabonate-1,4-lactone, 20% glycerol), sitting drop vapor diffuction, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.43 64.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.3 α = 90 b = 75.3 β = 90 c = 142.45 γ = 120
Symmetry Space Group P 32 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 CCD ADSC QUANTUM 315r MIRRORS 2011-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.925 65.212 99.8 0.138 7.3 5.9 36087 36087
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 1.92 2.03 99.9 0.021 2.106 0.4 5.7 5178
Refinement Statistics Diffraction ID Structure Solution 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4DNM 1.925 38.386 28155 28155 1421 77.86 0.1944 0.1944 0.1926 0.1885 0.2282 0.2193 random 32.2636
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] -0.2988 -0.2988 0.5977
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.164 f_angle_d 1.082 f_chiral_restr 0.072 f_bond_d 0.012 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2268 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 14
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction CBASS data collection MOSFLM data reduction PHENIX phasing