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Crystal structure of putative alpha-ribazole-5'-phosphate phosphatase CobC FROM Vibrio parahaemolyticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 5% ISOPROPANOL, 2000 MM AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 7.5
Crystal Properties Matthews coefficient Solvent content 6.2 80.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.215 α = 90 b = 107.215 β = 90 c = 206.717 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 315 MIRRORS 2009-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.61 50 99.9 0.132 5 6.5 37362 -0.5
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) 2.61 2.7 99.6 0.94 0.8 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.8 20 26642 849 90.51 0.26331 0.26275 0.2649 0.28009 0.2768 RANDOM 127.928
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] -4.25 -4.25 8.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.26 r_dihedral_angle_3_deg 20.321 r_dihedral_angle_4_deg 16.03 r_dihedral_angle_1_deg 6.92 r_scangle_it 6.262 r_scbond_it 3.932 r_mcangle_it 3.504 r_mcbond_it 1.895 r_angle_refined_deg 1.153 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.26 r_dihedral_angle_3_deg 20.321 r_dihedral_angle_4_deg 16.03 r_dihedral_angle_1_deg 6.92 r_scangle_it 6.262 r_scbond_it 3.932 r_mcangle_it 3.504 r_mcbond_it 1.895 r_angle_refined_deg 1.153 r_nbtor_refined 0.298 r_xyhbond_nbd_refined 0.131 r_nbd_refined 0.129 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.089 r_symmetry_vdw_refined 0.078 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_refined 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 3194 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose SHELXD phasing REFMAC refinement DENZO data reduction HKL-2000 data scaling