☰ Navigation Tabs
CRYSTAL STRUCTURE OF AN URONATE ISOMERASE (BH0493) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J5S PDB entry 1J5S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.33 277 NANODROP, 7.5% PEG 8000, 36.0% 2-methyl-2,4-pentanediol, 0.1M Sodium cacodylate pH 6.33, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.89 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 273.72 α = 90 b = 158.56 β = 116.03 c = 181.24 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-02-24 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97935 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 2 48.564 93.7 0.072 9.33 2.83 437594 25.43
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 2 2.11 72.2 0.442 2.39 2.58 45786
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 (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, MAD THROUGHOUT PDB entry 1J5S 2 48.564 437582 5300 97.54 0.149 0.149 0.148 0.1558 0.178 0.2322 THIN SHELLS 20.506
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] 0.41 -0.89 1.16 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 16.81 r_dihedral_angle_3_deg 13.025 r_scangle_it 6.513 r_dihedral_angle_1_deg 6.215 r_scbond_it 4.786 r_mcangle_it 2.382 r_angle_refined_deg 1.388 r_mcbond_it 1.33 r_angle_other_deg 0.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.084 r_dihedral_angle_4_deg 16.81 r_dihedral_angle_3_deg 13.025 r_scangle_it 6.513 r_dihedral_angle_1_deg 6.215 r_scbond_it 4.786 r_mcangle_it 2.382 r_angle_refined_deg 1.388 r_mcbond_it 1.33 r_angle_other_deg 0.955 r_mcbond_other 0.495 r_symmetry_vdw_other 0.301 r_nbd_refined 0.214 r_nbd_other 0.199 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.156 r_symmetry_vdw_refined 0.101 r_metal_ion_refined 0.091 r_chiral_restr 0.088 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 41334 Nucleic Acid Atoms Solvent Atoms 3732 Heterogen Atoms 327
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction MOLREP phasing SHELXD phasing autoSHARP phasing