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Structure of ribose 5-phosphate isomerase a from methanocaldococcus jannaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 oil batch (TERA) 4.75 298 20MM TRIS-HCL PH 8.0, 200MM NACL. 40% V/V 1,2-PROPANEDIOL, 0.1M ACETATE PH 4.5, 0.05M CA ACETATE, oil batch (TERA), temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.22 44.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.856 α = 90 b = 100.273 β = 92.54 c = 80.465 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 225 mm CCD mirrors 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.074 SRS PX10.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 30 98.5 0.104 0.087 13.6 8 94575 94575 17
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) 1.7 1.76 98.3 0.392 0.38 4 5.1 8356
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT 1KL5 1.78 30 81022 81022 4045 97.57 0.15 0.15 0.148 0.1564 0.188 0.1951 RANDOM 17.944
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] 0.42 0.66 -0.6 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.39 r_dihedral_angle_4_deg 15.181 r_dihedral_angle_3_deg 12.942 r_dihedral_angle_1_deg 6.038 r_scangle_it 3.246 r_scbond_it 2.346 r_angle_refined_deg 1.469 r_mcangle_it 1.31 r_mcbond_it 1.186 r_angle_other_deg 1.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.39 r_dihedral_angle_4_deg 15.181 r_dihedral_angle_3_deg 12.942 r_dihedral_angle_1_deg 6.038 r_scangle_it 3.246 r_scbond_it 2.346 r_angle_refined_deg 1.469 r_mcangle_it 1.31 r_mcbond_it 1.186 r_angle_other_deg 1.015 r_symmetry_vdw_refined 0.286 r_symmetry_vdw_other 0.267 r_mcbond_other 0.225 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.199 r_nbd_other 0.191 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.088 r_nbtor_other 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7259 Nucleic Acid Atoms Solvent Atoms 889 Heterogen Atoms 69
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOLREP phasing