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Crystal Structure of Native CaiB in complex with coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XK6 PDB ENTRY 1XK6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 294 1.35M Sodium citrate, 0.1 M Tris-Cl (pH 7.0), VAPOR DIFFUSION, temperature 21K
Crystal Properties Matthews coefficient Solvent content 3.59 65.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.76 α = 90 b = 87.76 β = 90 c = 164.45 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 100 CCD ADSC QUANTUM 4 2004-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 2.3 41.1 0.054 26.7 5.5 29328 28766
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.39 99 0.567 4.8 5.7
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 (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 1XK6 2.3 41.1 29328 27309 1457 98.08 0.19878 0.19674 0.1965 0.23713 0.2389 RANDOM 52.586
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.157 r_dihedral_angle_4_deg 15.911 r_dihedral_angle_3_deg 15.557 r_dihedral_angle_1_deg 5.235 r_scangle_it 2.519 r_scbond_it 1.681 r_angle_refined_deg 1.21 r_mcangle_it 0.881 r_mcbond_it 0.648 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.157 r_dihedral_angle_4_deg 15.911 r_dihedral_angle_3_deg 15.557 r_dihedral_angle_1_deg 5.235 r_scangle_it 2.519 r_scbond_it 1.681 r_angle_refined_deg 1.21 r_mcangle_it 0.881 r_mcbond_it 0.648 r_nbtor_refined 0.302 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.181 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 3028 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing