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Crystal structure of a putative ribose 5-phosphate isomerase (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PPW PDB entry 2PPW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 277 NANODROP, 0.2M LiNO3, 20.0% PEG 3350, No Buffer pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.754 α = 90 b = 109.462 β = 102.92 c = 167.569 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.81 49.147 96.9 0.063 8.69 330786 -3 22.954
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.87 97.2 0.429 2.3
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 PDB entry 2PPW 1.81 49.147 330758 16707 96.93 0.173 0.17 0.1781 0.22 0.2251 RANDOM 25.658
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] 1.88 0.77 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.673 r_dihedral_angle_3_deg 11.616 r_dihedral_angle_4_deg 11.224 r_scangle_it 7.71 r_scbond_it 5.503 r_dihedral_angle_1_deg 3.778 r_mcangle_it 3.186 r_mcbond_it 2.136 r_angle_refined_deg 1.709 r_angle_other_deg 1.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.673 r_dihedral_angle_3_deg 11.616 r_dihedral_angle_4_deg 11.224 r_scangle_it 7.71 r_scbond_it 5.503 r_dihedral_angle_1_deg 3.778 r_mcangle_it 3.186 r_mcbond_it 2.136 r_angle_refined_deg 1.709 r_angle_other_deg 1.547 r_mcbond_other 0.643 r_chiral_restr 0.095 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25574 Nucleic Acid Atoms Solvent Atoms 2655 Heterogen Atoms 276
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction MOLREP phasing