☰ Navigation Tabs
Crystal structure of Ribose-5-phosphate isomerase A from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ENQ PDB entry 3enq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Moledular Dimensions, Morpheus screen G4: 20mM each Na-Formate; NH4-Acetate; Na3-Citrate; NaKTartrate
(racemic); Na-Oxamate; 12.5% each MPD (racemic); PEG 1K; PEG 3350; 100mM Imidazole; MES (acid) pH 6.5; PsaeA.00944.a.B1.PS02170 at 29.9mg/ml; direct cryo; tray 258189, puck frv7-1
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.07 α = 90 b = 142.79 β = 90 c = 161.21 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX-300 2014-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.25 50 99.6 0.068 0.076 14 4.8 262311 261250 -3 8.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.28 99.9 0.495 0.555 3.22 4.8
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 PDB entry 3enq 1.25 45.649 1.34 261196 2000 99.59 0.1385 0.1383 0.1396 0.1574 0.1583 Random selection 14.3851
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 12.023 f_angle_d 1.108 f_chiral_restr 0.072 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6719 Nucleic Acid Atoms Solvent Atoms 1578 Heterogen Atoms 52
Software Software Software Name Purpose XDS data reduction PHASER phasing ARP model building Coot model building PHENIX refinement PDB_EXTRACT data extraction XDS data scaling