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Crystal structure of glucuronate isomerase from Caulobacter crescentus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JS5 PDB entry 1JS5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 294 1.0 M Sodium-potassium phosphate, pH 8.2, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.99 69.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.332 α = 90 b = 190.176 β = 90 c = 319.29 γ = 90
Symmetry Space Group F 2 2 2
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 MAR CCD 165 mm MIRRORS 2006-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97960 APS 31-ID
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 2.34 50 92.7 0.188 0.178 2.7 2.5 112315 112315 45
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 2.34 2.43 61.9 0.6 0.57 0.4 1.8
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 PDB entry 1JS5 2.34 20 99708 99708 3035 91.69 0.19972 0.19972 0.19818 0.1969 0.25125 0.2463 RANDOM 51.199
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] 1.73 -1.98 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.594 r_dihedral_angle_3_deg 18.542 r_dihedral_angle_4_deg 14.513 r_scangle_it 12.408 r_scbond_it 9.075 r_mcangle_it 7.327 r_dihedral_angle_1_deg 5.519 r_mcbond_it 4.984 r_angle_refined_deg 1.177 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.594 r_dihedral_angle_3_deg 18.542 r_dihedral_angle_4_deg 14.513 r_scangle_it 12.408 r_scbond_it 9.075 r_mcangle_it 7.327 r_dihedral_angle_1_deg 5.519 r_mcbond_it 4.984 r_angle_refined_deg 1.177 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.192 r_metal_ion_refined 0.163 r_xyhbond_nbd_refined 0.155 r_nbd_refined 0.141 r_symmetry_vdw_refined 0.089 r_chiral_restr 0.087 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11530 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 3
Software Software Software Name Purpose PHASER phasing REFMAC refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling