☰ Navigation Tabs
Crystal structure of prephenate dehydratase from brucella melitensis biovar abortus 2308 in complex with phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QMX 2QMX_B, 3MWB_A, 2QMW_A, 3LUY_A, 4LUB_A experimental model PDB 3LUY 2QMX_B, 3MWB_A, 2QMW_A, 3LUY_A, 4LUB_A experimental model PDB 4LUB 2QMX_B, 3MWB_A, 2QMW_A, 3LUY_A, 4LUB_A experimental model PDB 3MWB 2QMX_B, 3MWB_A, 2QMW_A, 3LUY_A, 4LUB_A experimental model PDB 2QMW 2QMX_B, 3MWB_A, 2QMW_A, 3LUY_A, 4LUB_A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 RigakuReagents PACT screen, condition E12:200mM sodium malonate, dibasic, 20% PEG 3350: BrabA.00146.a.A1.PW25617 at 28.9mg/ml: cryo: 20% EG: tray: 216998 e6, puck gej7-16.
Crystal Properties Matthews coefficient Solvent content 2.82 56.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 226.95 α = 90 b = 61.25 β = 112.95 c = 120.05 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 CCD ADSC QUANTUM 315r 2010-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.4 41.41 98.4 0.057 0.065 0.999 12.82 4.465 59038 60.259
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 99.3 0.546 0.619 0.966 2.33 4.609
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 2QMX_B, 3MWB_A, 2QMW_A, 3LUY_A, 4LUB_A 2.4 41.41 1.34 58845 1873 98.24 0.2083 0.2069 0.2079 0.2506 0.2515 0 70.4797
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.093 f_angle_d 0.783 f_chiral_restr 0.053 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8438 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MR-Rosetta phasing